What is Bacterial Comparative Genomics?

Comparative genomics involves the systematic comparison of genomes across different bacterial species or strains. This approach allows scientists to:

• Identify conserved and unique genes.

• Explore genetic determinants of pathogenicity.

• Understand bacterial evolution and phylogenetics.

• Investigate horizontal gene transfer and its role in antibiotic resistance.

Bioinformatics is central to these analyses, enabling the processing and interpretation of large-scale genomic data.

Key Steps in Bacterial Comparative Genomics

1. Genome Sequencing and Assembly: The process begins with obtaining high-quality bacterial genome sequences. Advances in next-generation sequencing (NGS) technologies have made it faster and more affordable to sequence bacterial genomes. Tools such as SPAdes and Velvet are commonly used for genome assembly.

2. Genome Annotation: Annotating a genome involves identifying genes, regulatory elements, and other genomic features. Automated tools like Prokka and RAST provide functional annotations, allowing researchers to predict the roles of genes and proteins.

3. Genome Alignment: Aligning genomes is crucial for identifying conserved regions, single-nucleotide polymorphisms (SNPs), and structural variations. Tools like Mauve and progressiveMauve are commonly employed for whole-genome alignments.

4. Comparative Analyses:

   • Core and Pan-genome Analysis: The core genome consists of genes shared across all strains of a species, while the pan-genome includes all genes found in any strain. Software like Roary and BPGA can perform core and pan-genome analyses.

   • Phylogenetic Analysis: Comparative genomics often involves reconstructing evolutionary relationships. Tools such as MEGA and IQ-TREE facilitate phylogenetic tree construction based on genomic data.

   • Functional Enrichment Analysis: To understand the biological significance of unique or shared genes, functional enrichment analysis using databases like GO (Gene Ontology) and KEGG is essential.

Here are some additional bioinformatics tools that can aid bacterial comparative genomics:

• OrthoFinder: For accurate ortholog identification across multiple genomes.

• PanOCT: Specifically designed for pan-genome clustering and annotation.

• FASTANI: A tool for calculating Average Nucleotide Identity (ANI) for microbial genome comparisons.

• CIRCOS: For visually comparing genomic data through circular genome plots.

• Galaxy Platform: A user-friendly web-based platform offering numerous genomic analysis tools.

• BLAST: Essential for sequence alignment and similarity searches.

• PhyloSift: Focused on phylogenetic analysis of microbial genomes using marker genes.

These tools, in combination with the methods discussed, provide a robust framework for conducting comprehensive comparative genomic studies.

Applications of Bacterial Comparative Genomics

1. Understanding Pathogenicity: Comparative genomics helps identify virulence factors that distinguish pathogenic strains from non-pathogenic relatives. For instance, comparing genomes of Escherichia coli strains has revealed key genetic determinants of pathogenicity in enterohemorrhagic strains.

2. Antibiotic Resistance Research: The spread of antibiotic resistance genes through horizontal gene transfer is a major global concern. Comparative analyses can trace the origins and dissemination of resistance genes, aiding in the development of countermeasures.

3. Microbial Ecology and Evolution: By studying genomic variations, researchers can understand how bacteria adapt to different environments. This is particularly relevant for extremophiles and symbiotic bacteria.

4. Vaccine Development: Identifying conserved antigens across pathogenic strains is critical for vaccine design. Comparative genomics has been instrumental in developing vaccines against pathogens like Neisseria meningitidis.

5. Biotechnology Applications: Comparative studies can uncover unique metabolic pathways in bacteria, paving the way for applications in bioremediation, synthetic biology, and industrial microbiology.

Challenges in Bacterial Comparative Genomics

While the field has made significant strides, several challenges remain:

• Data Overload: The rapid growth of sequencing data requires robust computational infrastructure and efficient algorithms.

• Genome Plasticity: High rates of horizontal gene transfer and genome rearrangements in bacteria complicate comparative analyses.

• Annotation Accuracy: Automated annotation tools are not infallible, and manual curation is often needed for high-confidence results.

• Interpreting Non-Coding Regions: Understanding the functional significance of non-coding genomic regions remains a challenge.

Future Directions

The integration of bacterial comparative genomics with other ‘omics’ approaches—such as transcriptomics, proteomics, and metabolomics—promises a more comprehensive understanding of bacterial biology. Additionally, advancements in machine learning and artificial intelligence are likely to further enhance bioinformatics analyses, enabling the prediction of complex phenotypes from genomic data.

Conclusion

Bacterial comparative genomics, driven by bioinformatics, continues to unravel the complexities of bacterial life. From combating antibiotic resistance to uncovering the secrets of microbial evolution, this interdisciplinary field holds immense potential for addressing pressing challenges in microbiology and beyond. As technology advances, so too will our ability to harness the power of comparative genomics for scientific and societal benefit.

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/23/14/1713.full

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

Align/Assemble to a reference
BFAST - Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA.
Bowtie - Ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Transformed (BWT) index. Link to discussion thread here. Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X.
BWA - Heng Lee's BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence. C++ source.
ELAND - Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.
Exonerate - Various forms of pairwise alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.
GenomeMapper - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. A tool created by the 1001 Genomes project. Source for POSIX.
GMAP - GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences. Developed by Thomas Wu and Colin Watanabe at Genentec. C/Perl for Unix.
gnumap - The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. It seeks to align reads from nonunique repeats using statistics. From authors at Brigham Young University. C source/Unix.
MAQ - Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina with preliminary functions to handle ABI SOLiD data. Written by Heng Li from the Sanger Centre. Features extensive supporting tools for DIP/SNP detection, etc. C++ source
MOSAIK - MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Features a number of support tools. Support for Roche FLX, Illumina, SOLiD, and Helicos. Written by Michael Strömberg at Boston College. Win/Linux/MacOSX
MrFAST and MrsFAST - mrFAST & mrsFAST are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. Robust to INDELs and MrsFAST has a bisulphite mode. Authors are from the University of Washington. C as source.
MUMmer - MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Version 3.0 was developed by Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L Salzberg - most of whom are at The Institute for Genomic Research in Maryland, USA. POSIX OS required.
Novocraft - Tools for reference alignment of paired-end and single-end Illumina reads. Uses a Needleman-Wunsch algorithm. Can support Bis-Seq. Commercial. Available free for evaluation, educational use and for use on open not-for-profit projects. Requires Linux or Mac OS X.
PASS - It supports Illumina, SOLiD and Roche-FLX data formats and allows the user to modulate very finely the sensitivity of the alignments. Spaced seed intial filter, then NW dynamic algorithm to a SW(like) local alignment. Authors are from CRIBI in Italy. Win/Linux.
RMAP - Assembles 20 - 64 bp Illumina reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.
SeqMap - Supports up to 5 or more bp mismatches/INDELs. Highly tunable. Written by Hui Jiang from the Wong lab at Stanford. Builds available for most OS's.
SHRiMP - Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. POSIX.
Slider- An application for the Illumina Sequence Analyzer output that uses the probability files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Authors are from BCGSC. Paper is here.
SOAP - SOAP (Short Oligonucleotide Alignment Program). A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute. C++, POSIX.
SSAHA - SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a tool for rapidly finding near exact matches in DNA or protein databases using a hash table. Developed at the Sanger Centre by Zemin Ning, Anthony Cox and James Mullikin. C++ for Linux/Alpha.
SOCS - Aligns SOLiD data. SOCS is built on an iterative variation of the Rabin-Karp string search algorithm, which uses hashing to reduce the set of possible matches, drastically increasing search speed. Authors are Ondov B, Varadarajan A, Passalacqua KD and Bergman NH.
SWIFT - The SWIFT suit is a software collection for fast index-based sequence comparison. It contains: SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences. SWIFT BALSAM — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmussen (SWIFT) and Wolfgang Gerlach (SWIFT BALSAM)
SXOligoSearch - SXOligoSearch is a commercial platform offered by the Malaysian based Synamatix. Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent.
Vmatch - A versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements. Essentially a large string matching toolbox. POSIX.
Zoom - ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority. Commercial. Supports Illumina and SOLiD data.
NCGR uses GMAP (http://www.gene.com/share/gmap/) to alignment Solexa reads. GMAP is free, though.
Exonerate (http://www.ebi.ac.uk/~guy/exonerate/)
MUMmer (http://mummer.sourceforge.net/)
The mapping short reads called gnumap (http://dna.cs.byu.edu/gnumap/) made to increase the accuracy with duplicate matches. Open source, creates viewable output (with Affy's Integrated Genome Browser), and produces results very similar to novocraft's.
SOCS (short oligonucleotides in color space)
BFAST https://secure.genome.ucla.edu/index.php/BFAST

De novo Align/Assemble
ABySS - Assembly By Short Sequences. ABySS is a de novo sequence assembler that is designed for very short reads. The single-processor version is useful for assembling genomes up to 40-50 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. By Simpson JT and others at the Canada's Michael Smith Genome Sciences Centre. C++ as source.
ALLPATHS - ALLPATHS: De novo assembly of whole-genome shotgun microreads. ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities, such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. Broad Institute.
Edena - Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. By D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel. Linux/Win.
EULER-SR - Short read de novo assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach.
MIRA2 - MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.
SEQAN - A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads. By Tobias Rausch and others. C++, Linux/Win.
SHARCGS - De novo assembly of short reads. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics.
SSAKE - The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux.
SOAPdenovo - Part of the SOAP suite. See above.
VCAKE - De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.
Velvet - Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).
SOAP (http://soap.genomics.org.cn) by Ruiqiang Li, as has been pointed by ECO.
Euler-SR (Euler-Short Reads Assembly, http://euler-assembler.ucsd.edu/portal/) by Mark J. Chaisson and Pavel A. Pevzner from UCSD. (published in Genome Research)
RMAP (A program for mapping Solexa reads, http://rulai.cshl.edu/rmap/) by Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics)
Short read aligner called Bowtie (http://bowtie-bio.sourceforge.net/) designed for fast mapping of Illumina reads

SNP/Indel Discovery
ssahaSNP - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac
PolyBayesShort - A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32.
PyroBayes - PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College.
Maq is also able to find SNPs with its own alignment. It has a graphical viewer, but again for its own alignment format.
SSAHA has been optimized for short-reads, too. But yes, SSAHASNP appears in your "SNP/INDEL discovery" category.

Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database
EagleView - An information-rich genome assembler viewer. EagleView can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College.
LookSeq - LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. LookSeq supports multiple sequencing technologies, alignment sources, and viewing modes; low or high-depth read pileups; and easy visualization of putative single nucleotide and structural variation. From the Sanger Centre.
MapView - MapView: visualization of short reads alignment on desktop computer. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China. Linux.
SAM - Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux.
STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here
XMatchView - A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux.

Counting e.g. CHiP-Seq, Bis-Seq, CNV-Seq
BS-Seq - The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.
CHiPSeq - Program used by Johnson et al. (2007) in their Science publication
CNV-Seq - CNV-seq, a new method to detect copy number variation using high-throughput sequencing. Chao Xie and Martti T Tammi at the National University of Singapore. Perl/R.
FindPeaks - perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest. Original algorithm by Matthew Bainbridge, in collaboration with Gordon Robertson. Current code and implementation by Anthony Fejes. Authors are from the Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of the Vancouver Short Read Analysis Package
MACS - Model-based Analysis for ChIP-Seq. MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. Written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab.
PeakSeq - PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls. a two-pass approach for scoring ChIP-Seq data relative to controls. The first pass identifies putative binding sites and compensates for variation in the mappability of sequences across the genome. The second pass filters out sites that are not significantly enriched compared to the normalized input DNA and computes a precise enrichment and significance. By Rozowsky J et al. C/Perl.
QuEST - Quantitative Enrichment of Sequence Tags. Sidow and Myers Labs at Stanford. From the 2008 publication Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. (C++)
SISSRs - Site Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH. Perl.
SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap/) - work like ELand, can do 3 or more bp mismatches and also insdel
ChIPSeq analysis is:  http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/

See also this thread for ChIP-Seq, until I get time to update this list.

Alternate Base Calling
Rolexa - R-based framework for base calling of Solexa data. Project publication
Alta-cyclic - "a novel Illumina Genome-Analyzer (Solexa) base caller"

Transcriptomics
ERANGE - Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Supports Bowtie, BLAT and ELAND. From the Wold lab.
G-Mo.R-Se - G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads. From CNS in France.
MapNext - MapNext: A software tool for spliced and unspliced alignments and SNP detection of short sequence reads. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China.
QPalma - Optimal Spliced Alignments of Short Sequence Reads. Authors are Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, and Gunnar Rätsch. A paper is available.
RSAT - RSAT: RNA-Seq Analysis Tools. RNASAT is developed and maintained by Hui Jiang at Stanford University.
TopHat - TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland and the University of California, Berkeley
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer http://www.biomedcentral.com/1471-2105/14/S7/S10

Reference

Illumina has a software list: http://www.illumina.com/pagesnrn.ilmn?ID=245.

Some softwares in his blog (http://www.fejes.ca/labels/DNA.html)

http://seqanswers.com/wiki/Software

More at https://gatb.inria.fr/

Address of the bookmark: https://gatb.inria.fr/

In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later characterized and placed into five categories:

Simple Repeats - Duplications of simple sets of DNA bases (typically 1-5bp) such as A, CA, CGG etc.
Tandem Repeats - Typically found at the centromeres and telomeres of chromosomes these are duplications of more complex 100-200 base sequences.
Segmental Duplications - Large blocks of 10-300 kilobases which are that have been copied to another region of the genome.
Interspersed Repeats
Processed Pseudogenes, Retrotranscripts, SINES - Non-functional copies of RNA genes which have been reintegrated into the genome with the assitance of a reverse transcriptase.
DNA Transposons
Retrovirus Retrotransposons
Non-Retrovirus Retrotransposons ( LINES )

Currently up to 50% of the human genome is repetitive in nature and as improvements are made in detection methods this number is expected to increase.

On the other hand; In genetics, the term palindrome refers to a sequence of nucleotides along a DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) strand that contains the same series of nitrogenous bases regardless from which direction the strand is analyzed. Akin to a language palindrome—wherein a word or phrase is spelled the same left-to-right as right-to-left (e.g., the word RADAR or the phrase "able was I ere I saw elba")—with genetic palindromes it does not matter whether the nucleic acid strand is read starting from the 3' (three prime) end or the 5' (five prime) end of the strand.

Recent research on palindromes centers on understanding palindrome formation during gene amplification. Other studies have attempted to relate palindrome formation to molecular mechanisms involved in double stranded breaks and in the formation of inverted repeats. Assisted by high speed computers, other groups of scientists link palindrome formation to the conservation of genetic information.

Related to the direction of transcription by RNA polymerase, DNA strands have upstream and downstream terminus defined by differing chemical groups at each end. The ends of each strand of DNA or RNA are termed the 5' (phosphate bound to the 5' position carbon) and 3' (phosphate bound to the 3' carbon) ends to indicate a polarity within the molecule. Using the letters A, T, C, G, to represent the nitrogenous bases adenine, thymine, cytosine, and guanine found in DNA, and the letters A, U, C, G to represent the nitrogenous bases adenine, uracil, cytosine, guanine found in RNA (Note that uracil in RNA replaces the thymine found in DNA), geneticists usually represent DNA by a series of base codes (e.g., 5' AATCGGATTGCA 3'). The base codes are usually arranged from the 5' end to the 3' end.

Because of specific base pairing in DNA (i.e., adenine (A) always bonds with (thymine (T) and cytosine (C) always bonds with guanine (G)) the complimentary stand to the sequence 5' AATCGGATTGCA 3' would be 3' TTAGCCTAACGT 5'.

With palindromes the sequences on the complimentary strands read the same in either direction. For example, a sequence of 5' GAATTC3' on one strand would be complimented by a 3' CTTAAG 5' strand. In either case, when either strand is read from the 5' prime end the sequence is GAATTC. Another example of a palindrome would be the sequence 5' CGAAGC 3' that, when reversed, still reads CGAAGC.

Palindromes are important sequences within nucleic acids. Often they are the site of binding for specific enzymes (e.g., restriction endobucleases) designed to cut the DNA strands at specific locations (i.e., at palindromes).

Palindromes may arise from brakeage and chromosomal inversions that form inverted repeats that compliment each other. When a palindrome results from an inversion, it is often referred to as an inverted repeat. For example, the sequence 5' CGAAGC 3', if inverted (reversed 180°), still reads CGAAGC.

The European Molecular Biology Open Software Suite (EMBOSS) includes some basic tools for finding tandem repeats and inverted repeats (see B.6.22. Applications in group Nucleic:repeats). There are many on-line services providing the EMBOSS tools, for example:

• Wageningen Bioinformatics Webportal EMBOSS explorer
• Mobyle@Pasteur
• Soaplab2 Web Services at Vital-IT

For more sophisticated repeat finding you will want to look at tools using Repbase for example:

• CENSOR
  • CENSOR@GIRI
  • CENSOR@EMBL-EBI
• RepeatMasker
• MUMmer (scan_for_match)
• Emboss Palindrome

Other nucleotide repeat finding methods found by a couple of web searches:

• Tandem Repeats Finder
• RECON
• RepeatRunner
• REPuter
• Imperfect Microsatellite Extractor (IMEx)
• Spectral Repeat Finder (SRF)
• REPFIND
• CRISPRfinder
• GrailEXP
• CONREPP
• find_palindromes
• Palindrome
• EMBOSS Palindrome
• Palindrome Search

We therefore list many genomle assembly tools here. We mainly reported for the assembly of genomes while the others are designed aiming at handling complex genomes.

• TriMetAss 1.2 – The Trinity-based Iterative Metagenomics Assembler
  • TriMetAss is an extension to the Trinity software [1], which can assemble select regions surrounding interesting features in metagenomic data. The software is particularly useful for very common and well-conserved genes (and – in theory – non-coding regions) that can occur in multiple contexts in the microbial community under study. It uses Vmatch [2] to extend seed reads (or contigs generated by another assembler) into longer contigs, by iteratively calling Vmatch and Trinity, until some stop criteria are met. Currently, TriMetAss lacks a thorough documentation, but you can direct questions to me if the README.txt file and the “-h” option is not sufficient to understand the software.
    
    
• OMWare 1.0 – Efficient Assembly of Genome-wide Physical Maps

  • The purpose of this Python module is help scientists use optical map data.
    Once complete, it will encapsulate and abstractify optical maps and their most common manipulations as they exist in a variety of formats.

• LightAssembler – Lightweight Resources Assembly Algorithm

  • Lightweight resources assembly algorithm for high-throughput sequencing reads.
    System requirements
    64-bit machine with g++ compiler or gcc in general, pthreads,and zlib libraries.

• QUAST 4.1 – Quality Assessment Tool for Genome Assemblies

  • QUAST evaluates genome assemblies.
    QUAST works both with and without a reference genome. 
    The tool accepts multiple assemblies, thus is suitable for comparison.

• DNA Baser 4.36 – DNA Sequence Assembly & Analysis
  • DNA Sequence Assembler is revolutionary bioinformatics software for automatic DNA sequence assembly , DNA sequence analysis, contig editing, file format conversion and mutation detection.
    
    
• COCACOLA – Binning Metagenomic Contigs using Sequence COmposition, Read CoverAge, CO-alignment, and Paired-end Read LinkAge
  
  • COCACOLA: a general framework for binning contigs in metagenomic studies incorporating read COverage, CorrelAtion, sequence COmposition and paired-end read LinkAge
    
    
• MaxBin 2.2 – Binning Assembled Metagenomic Sequences
  • MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. 
    
    
• GAML 0.1 – Genome Assembly by Maximum Likelihood
  
  • GAML is a prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of indvidual sequencing technologies. It can combine datasets produced by different technologies (currently Illumina, 454 and Pacific Biosciences).
    
    
• NanoMark – DNA Assembly Benchmark for Nanopore long reads

  • DNA Assembly Benchmark for Nanopore long reads
    A system for benchmarking DNA assembly tools, based on 3rd generation sequencers.

• ARC 1.1.4-beta – Assembly by Reduced Complexity

  • ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: 
    1.Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
    2.Reducing/removing reference bias as compared to mapping based approaches.

• TransPS 1.1.0 – Transcriptome Post Scaffolding
  • TransPS is a pipeline for post-processing of pre-assembled transcriptomes using reference based method. It applies an align-layout-consensus structure, consisting of three major stages. First, query sequences are aligned with a reference genome. Second, query sequences are ordered based on the alignment to the reference. Third, non-redundant sequences matched to the same gene of reference genome are scaffolded into one contig. 
    
    
• assemblyManager – Computing the Robotic Commands for 2ab Assembly
  • Clotho provides persistence to such objects through relational databases that at least partially correspond the Clotho data model. Beyond database access and data model API support, Clotho Apps provide more specific functionality to Clotho such as viewing and editing data, running simulations, and automating various tasks. When thinking about Clotho Apps, an appropriate analogy would be Apps running on the Android operating system rather than the add-ons that extend the functionality of Firefox
    
    
• BinPacker 1.1 – Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
  • BinPacker is a novel de novo assembler by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems
    
    
• FermiKit 0.13 – De novo Assembly based Variant Calling pipeline for Illumina Short Reads
  • FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. It assembles reads into unitigs, maps them to the reference genome and then calls variants from the alignment to an accuracy comparable to conventional mapping based pipelines (see evaluation in the tex directory). The assembly does not only encode SNPs and short INDELs, but also retains long deletions, novel sequence insertions, translocations and copy numbers
    
    
• REPdenovo – A tool to Construct Repeats directly from Raw Reads

  • REPdenovo is designed for constructing repeats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo provides many functionalities, and can generate much longer repeats than existing tools. The overall pipeline is shown in the mannual file. REPdenovo supports the following main functionalities.
    1.Assembly. This step performs k-mer counting. Then we find frequent k-mers whose frequencies are over certain threshold. We then assemble these frequent k-mers into consensus repeats (in the form of contigs). Then we merge the constructed contigs to more completeness ones.
    2.Scaffolding. We use paired-end reads to connect repeat contigs into scaffolds, also provide the average coverage (indicates the copy number) for each constructed repeats.

• Xander – Gene-targeted Metagenomic Assembler
  • Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. We present a novel method for targeting assembly of specific protein-coding genes using a graph structure combining both de Bruijn graphs and protein HMMs. The inclusion of HMM information guides the assembly, with concomitant gene annotation. 
    
    
• SWAP-Assembler 2 – A scalable and fully parallelized Genome Assembler
  • There is a growing gap between the output of new generation massively parallel sequencing machines and the ability to process and analyze the sequencing data. We present SWAP-Assembler, a scalable and fully parallelized genome assembler designed for massive sequencing data. Intend of using traditional de Bruijn Graph, SWAP-Assembler adopts multi-step bi-directed graph (MSG). With MSG, the standard genome assembly (SGA) is equivalent to the edge merging operations in a semi-group. Then a computation model, SWAP, is designed to parallelize semi-group computation. Experimental results showed that SWAP-Assembler is the fastest and most efficient assemblers ever, it can generated contigs with highest accuracy over all five selected assemblers and longest contig N50 in all selected parallel assemblers. Specially, in the scalability test, SWAP-Assembler can scales up to 1024 cores when processing Fish and Yanhuang dataset, and finishes the assembly work in only 15 and 29 minutes respecitively
    
    
• TGNet – Visualization and Quality Assessment of de novo Genome Assemblies
  • TGNet is a Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly.
    
    
• Circlator 1.1.3 – A tool to Circularize Genome Assemblies
  • A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. 
    
    
• misFinder v0.4.05.05 – Identify Mis-assemblies in an unbiased manner using Reference and Paired-end Reads
  • misFinder is a tool that aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their mis-assembled positions to improve the assembly accuracy for downstream analysis. It combines the information of reference (or close related reference) genome and aligned paired-end reads to the assembled sequence. Structure variation and mis-assembly can be detected by comparing the reference genome and assembled sequence.
    
    
• Scaffold_builder v2.2 – Order Contigs generated by draft sequencing along a Reference Sequence
  • The abundance of repeat elements in genomes can impede the assembly of a single sequence. The tool Scaffold_builder was designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.
    
    
• Rnnotator 3.5.0 – de novo Transcriptome Assembly pipeline from stranded RNA-Seq reads
  • Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. The contigs produced by Rnnotator are highly accurate and reconstruct full-length genes when transcripts are sequenced sufficiently deep, roughly 30X for a given transcript. Rnnotator was designed to assemble Illumina single or paired-end reads. Rnnotator is also able to incorporate strand-specific RNA-Seq reads into the assembly in order to further improve the assembly.
    
    
• SATRAP 0.2 – SOLiD Assembler TRAnslation Program

  • A color space assembly must be translated into bases before applying bioinformatics analyses. SATRAP is designed to accomplish this important task adopting a very efficient strategy. The package integrates the Oases pipeline and several optimizations specifically designed for color space management. All steps of the pipeline allow to produce a SOLiD de novo transcriptome assembly and the subsequent color space translation. Alternatively, SATRAP can be used as a stand alone program to perform color space translation for either RNA-seq or DNA-seq SOLiD assemblies.

• Bandage v0.7.1 – Navigating De novo Assembly Graphs Easily
  • Bandage is a program for visualising de novo assembly graphs. By displaying connections which are not present in the contigs file, Bandage opens up new possibilities for analysing de novo assemblies.
    
    
• HapCol 1.1.1 – Haplotype Assembly from Long Gapless Reads
  • A fast and memory-efficient method for haplotype assembly from long gapless reads, like those produced by SMRT sequencing technologies (PacBio RS II) and Oxford Nanopore flow cell technologies (MinION).
    
    
• REAGO 1.1 – REconstruct 16S ribosomal RNA Genes from MetagenOmic data
  
  • an assembly tool for 16S ribosomal RNA recovery from metagenomic data
    
    
• FGAP 1.8.1 – Automated Gap Closing tool
  • FGAP aims to improve genome sequences by merging alternative assemblies or incorporating alternative data, analyzing the gap region and indicating the best sequence to close the gap.
    
    
• DETONATE 1.10 – DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation
  • DETONATE consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
    
    
• Trinity 2.1.1 – RNA-Seq De novo Assembly
  
  • Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.
    
    
• IsoSCM 2.0.11 – Transcript Assembly tool using Multiple Change-point Inference to improve 3’UTR Annotation
  • IsoSCM (Isoform Structural Change Model) is a new method for transcript assembly  that incorporates change-point analysis to improve the 3′ UTR annotation process.
    
    
• IVA 1.0.3 – Iterative Virus Assembler
  • IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.
    
    
• SFA-SPA 0.2.1 – A Suffix Array based Short Peptide Assembler for Metagenomic Data
  • SFA-SPA is a suffix array based short peptide assembler for metagenomic data
    
    
• RAMPART 0.12.2 – A Workflow Management System for de novo Genome Assembly
  • RAMPART is a de novo assembly pipeline that makes use of third party-tools and High Performance Computing resources. It can be used as a single interface to several popular assemblers, and can perform automated comparison and analysis of any generated assemblies
    
    
• Celera Assembler 8.3 – Whole Genome Shotgun Assembler
  • Celera Assembler (wgs-assembler) is scientific software for DNA research. It can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler has enabled discovery in microbial genomes, large eukaryotic genomes, diploid genomes, and genomes from environmental samples. Celera Assembler contributed the first diploid sequence of an individual human, and metagenomics assemblies of the Global Ocean Sampling
    
    
• A5-miseq 20150522 – de novo Assembly & Analysis of Illumina Sequence data
  • de novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system
    
    
• Trans-ABySS 1.5.3 – Analyze ABySS multi-k-assembled Shotgun Transcriptome Data.
  • Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. The pipeline accepts assemblies that were generated across a wide range of k values in order to address variable transcript expression levels. It first filters and merges the multi-k assemblies, generating a much smaller set of nonredundant contigs. It contains scripts that map assembled contigs to known transcripts, currently supporting Blat and Exonerate contig-to-genome aligners. It identifies novel splicing events like exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. Its scripts can also estimate gene expression levels, identify candidate polyadenylation sites, and identify candidate gene-fusion events.
    
    
• SAT-Assembler 20160120 – Scalable and Accurate Targeted Gene Assembly Tool
  • SAT-Assembler can perform targeted gene assembly for both RNA-Seq and metagenomic data. It addresses the above challenges of de novo assembly of large scale NGS data by conducting family-specic gene assembly, homology-guided overlap graph construction, and careful graph traversal.
    
    
• Opera 2.0.2 – Sequence Assembly Program
  • Opera (Optimal Paired-End Read Assembler) is a sequence assembly program . It uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.
    
    
• Sequencher 5.4.1 – DNA Sequence Assembly and Analysis
  • Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago, Sequencher is currently used for sequence analysis tasks in every major genomic and pharmaceutical company as well as numerous academic and government labs in over 40 countries around the world. Life Science researchers use Sequencher for many diverse DNA sequence analysis applications including de novo gene sequencing, mutation detection, forensic human identification, systematics, and more.
    
    
• Minia 2.0.3 – Short-read Assembler based on a de Bruijn graph
  • Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day
    
    
• MaSuRCA 3.1.3 – Whole Genome Short Read Assembler
  • MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).
    
    
• KmerGenie 1.6982 – K-mer size Selection for Genome Assembly
  • KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie’s choices lead to assemblies that are close to the best possible over all k-mer lengths.
    
    
• pilon v1.16 – Automated Assembly Improvement
  • pilon uses read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.
    
    
• Phred/Phrap/Consed 29.0 – DNA Sequence Assembler & Finishing Tools
  
  • phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets.
    
    
• CLC Genomics Workbench 8.5.1 – Assembly & Analysis of Sequencing Data
  • CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.
    
    
• Metassembler 1.5 – Combines multiple Whole Genome de novo Assemblies into a combined Consensus Assembly
  • Metassembler is a software package for reconciling assemblies produced by de novo short-read assemblers such as SOAPdenovo and ALLPATHS-LG. The goal of assembly reconciliation, or “metassembly,” is to combine multiple assemblies into a single genome that is superior to all of its constituents
    
    
• Tablet 1.15.09.01 – Next Generation Sequence Assembly Visualization
  • Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine.
    
    
• ABySS 1.9.0 – de novo, parallel, paired-end Sequence Assembler
  • ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
    
    
• CLEAT 2.0 – Identifies 3′ UTR Ends of Transcripts in de novo RNA-Seq Assemblies
  • CLEAT is a post-processing tool for CLEavage site Analysis of Transcriptomes. CLEAT is designed to work on trans-ABySS output.
    
    
• StriDe – novel Assembler
  • The StriDe Assembler integrates string and de Bruijn graph by decomposing reads within error-prone regions, while extending paire-end read into long reads for assembly through repetitive regions.
    
    
• REAPR 1.0.18 – Genome Assembly Evaluation
  • REAPR (Recognising Errors in Assemblies using Paired Reads) is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.
    
    
• GapFiller 1.10 – Close Gaps within Pre-assembled Scaffolds
  • GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds. It is unique in offering the possibility to manually control the gapclosure process. By using the distance information of paired-read data, GapFiller seeks to close the gap from each edge in an iterative manner. From a good number of tests we see the program yields excellent results both on bacterial en eukaryotic  datasets. The command-line Perl script and additional files van be downloaded below. The input data is given by pre-assembled scaffold sequences (FASTA) and NGS paired-read data (FASTA or FASTQ).
    
    
• SSAKE 3.8.4 – Assembling Millions of short DNA Sequences
  • SSAKE is a genomics application for assembling millions of very short DNA sequences.SSAKE is designed to help leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets.
    
    
• SGA 0.10.14 – String Graph Assembler
  • SGA is a de novo assembler designed to assemble large genomes from high coverage short read data. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
    
    
• r2cat – Synteny Plots & Comparative Assembly
  
  • r2cat (related reference based contig arrangement tool) can be used to order a set of contigs with respect to a single reference genome. This is done by mapping the contigs onto the reference using a q-gram filter. The mapping is visualized in a synteny plot.
    
    
• TASR 1.6 – Targeted Assembly of Sequence Reads
  • TASR (Targeted Assembly of Sequence Reads)  is a genomics application that allows hypothesis-based interrogation of genomic regions (sequence targets) of interest.
    
    
• Rainbow v2.0.4 – Clustering and Assembling Short Reads, especially for RAD
  • Rainbow package consists of several programs used for RAD-seq related clustering and de novo assembly.
    
    
• CAFTOOLS 2.0.2 – Tools for the Common Assembly Format (CAF)
  • CAFTOOLS comprises a set of libraries and programs for manipulating DNA sequence assemblies using CAF files, a comprehensive representation of a sequence assembly as a text file.
• Gap Resolution – Improving Newbler Genome Assemblies. Gap Resolution was developed by DOE Joint Genome Institute to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA.
  
  
• Meraculous 2.0.5 – De novo Genome Assembler from Short Reads
  • Meraculous is a new algorithm for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis.
    
    
• COPE 1.2.5 – Pair-end Reads Connection tool to facilitate Genome Assembly
  • COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research.
    
    
• PEAR 0.9.6 – Pair-End reads AssembleR
  • PEAR is an ultrafast, memory-efficient and highly accurate pair-end reads assembler. It is fully parallelized and can run with as low as just a few kilobytes of memory.
    
    
• EBARDenovo 2.0.1 – Highly-accurate de novo Assembler of Paired-end RNA-Seq
  • EBARDenovo is a highly-accurate search-based de novo assembler of paired-end RNA-Seq for advance transcriptomic study.
    
    
• EagleView 2.2 – Genome Assembler Viewer
  • EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation.
    
    
• MAIA 0.5 – Integrating Genome Assemblies

  • MAIA (Multiple Assembly IntegrAtion) is an algorithm to integrate multiple genome assemblies. For example, assemblies originating from:
    – Different runs of a de novo assembler
    – Assemblies of different data types
    – Comparative assemblies

• InteMAP 1.0 – Integrated Metagenomic Assembly pipeline for NGS Short Reads
  
  • InteMAP is a pipeline which integrates individual assemblers for assembling metagenomic short sequencing reads.
    
    
• MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads
  • MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.
    
    
• Phusion 2.1c – Assembly Genome Sequences from Whole Genome Shotgun(WGS) Reads
  • Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads.
    
    
• CodonCode Aligner 6.0.2 – DNA Sequence Assembly & Alignment
  • CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. Aligner is compatible with Phred-Phrap and fully supports sequence quality scores, while offering a familiar, easy-to-learn user interface.
    
    
• Cerulean 0.1.1 – Hybrid Genome Assembler
  • Cerulean is a hybrid assembly using high throughput short and long reads
    
    
• Ragout 1.2 – Tool for Reference-assisted Assembly
  • Ragout (Reference-Assisted Genome Ordering UTility) is a tool for assisted assembly using multiple references. It takes a short read assembly (a set of contigs), a set of related references and a corresponding phylogenetic tree and then assembles the contigs into scaffolds.
    
    
• laSV 1.0.2 – Local Assembly based Structural Variation Discovery tool
  • laSV is a software that employs a local de novo assembly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets.
    
    
• SPAdes 3.6.2 – Single-cell Genome Assembler
  • SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
    
    
• PERGA 0.5.03.02 – Paired End Reads Guided Assembler
  • PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds.
    
    
• Telescoper 0.2 – De novo Assembly Algorithm
  • Telescoper is a local assembly algorithm designed for short-reads from NGS platforms such as Illumina. The reads must come from two libraries: one short insert, and one long insert.
    
    
• MetaCompass 1.0 – Comparative Assembly of Metagenomic Sequences
  • MetaCompass is a software package for comparative assembly of metagenomic reads. MetaCompass achieves comparable assembly performance to the state of the art de novo assemblers, but these two different approaches complement each other a lot. So combining contigs between MetaCompass and other independent de novo assemblers give us the best overall metagenomic assembly.
    
    
• SCARF – Scaffolded and Corrected Assembly of Roche 454
  • SCARF is a next-gen sequence assembly tool for evolutionary genomics. Designed especially for assembling 454 EST sequences against high quality reference sequences from related species.
    
    
• MetaCAA – Assembly of Metagenomic Datasets
  • MetaCAA is a sequence-assembly tool specifically intended for metagenomes.
    
    
• Contiguity 1.0.4 – Contig Adjacency Graph Construction and Visualisation
  • Contiguity is interactive software for the visualization and manipulation of de novo genome assemblies.
    
    
• ScaffoldScaffolder 0.1 – Solving Contig Orientation via Bidirected to Directed Graph Reduction
  • ScaffoldScaffolder is a stand-alone scaffolding algorithm which was designed specifically for scaffolding diploid genomes.
    
    
• HaploClique 0.1 – Viral Quasispecies Assembly from Paired-end data
  • HaploClique is a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.
    
    
• TAG 0.91 – Transcript Assembly by Mapping Reads to Graphs
  • TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference
    
    
• EPGA2 – De Novo Assembler
  • EPGA2 updates some modules in EPGA which can improve memory efficiency in genome asssembly.
    
    
• GMcloser 1.5.1 / GMvalue 1.3 – Closing the Gaps in Scaffolds with Preassembled Contigs
  • GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.
    
    
• SLICEMBLER – Meta-assembler Designed for Ultra-deep Sequencing data
  • SLICEMBLER is a meta-assembler designed for ultra-deep sequencing data
    
    
• SEQLandscape v1 – Generation and Visualization of Sequence Landscape

  • SEQLandscape is an application allowing the generation and visualization of a sequence landscape. HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly.

• misSEQuel v1.0beta – Misassembly Detection in Draft Genomes
  • misSEQuel is a software that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data.
    
    
• Dawg 1.2 – Simulating Sequence Evolution
  • Dawg (DNA Assembly with Gaps) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation.
    
    
• BUSCO v1.1b1 – Assessing Genome Assembly and Annotation Completeness with Single-copy Orthologs
  • BUSCO completeness assessment employs sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content.
    
    
• FinisherSC 2.0 – A Repeat-aware tool for upgrading de-novo Assembly using Long Reads
  • FinisherSC is a repeat-aware and scalable tool for upgrading de-novo assembly using long reads.
    
    
• WhatsHap – Haplotype Assembly for Future-Generation Sequencing Reads
  • WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
    
    
• Compartmentalized Assembler – Assembly of Physical Maps
  • Compartmentalized assembler is a novel method for the assemlby of high quality physical maps from fingerprinted clones.
    
    
• Elviz – Exploration of Metagenomic Assemblies
  • Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenome data and their complex metadata.
    
    
• SSP – de novo Transcriptome Assembler
  • SSP is a de novo transcriptome assembler that assembles RNA-seq reads into transcripts. SSP aims to reconstructs all the alternatively spliced isoforms and estimates the expression level of them.
    
    
• VirAmp – Galaxy-based Viral Genome Assembly pipeline
  • VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. VirAmp is a collection of existing tools, combined into a single Galaxy interface. Users without further computational knowledge can easily operate the pipeline.
    
    
• aTRAM 1.04 – automated Target Restricted Assembly Method
  • aTRAM performs targeted de novo assembly of loci from paired-end Illumina runs.
    
    
• Ray 2.3.1 – Parallel Genome Assemblies for Parallel DNA sequencing
  • Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.
    
    
• CAR – Contig Assembly of Prokaryotic Draft Genomes Using Rearrangements
  • CAR is an efficient and more accurate tool for assembling contigs of a prokaryotic draft genome based on a reference genome.
    
    
• VTBuilder – Assembly of Multi Isoform Transcriptomes
  • VTBuilder is a tool for the inference of non-chimeric contigs from read data that has been sequenced from complex multi-isoformic transcriptomes, such as snake venom glands, or rapidly evolving viral populations, such as HIV-1.
    
    
• TruHmm – TRanscription Unit Assembly by a Hidden Markov model
  • TruHmm is a reference based transcriptome assembler for prokaryotes, and is suitable for assembling transcripts for directional RNA-seq library.
    
    
• Bridger 20141201 – RNA-Seq Assembly
  • Bridger is a new de novo transcriptome assembler which takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers.
    
    
• GRASP 0.0.4 – Guided Reference-based Assembly of Short Peptides
  • GRASP is a gene annotation tool for metagenomic studies. GRASP assembles the fragmented short-peptides, which are called from the NGS reads, and aligns the assembled contigs to the query reference protein. GRASP achieves much higher sensitivity than BLASTP for gene annotation purpose.
    
    
• Cortex 1.05.21 – Genome Assembly and Variation Analysis
  • Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. There are two main executables, being developed in parallel streams: cortex_con (primary contact Mario Caccamo) is for consensus genome assembly, and cortex_var (primary contact Zamin Iqbal) is for variation and population assembly.
    
    
• MEGAHIT v0.1.4 – Large and Complex Metagenomics Assembly via Succinct de Bruijn graph
  • MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.
    
    
• CISA 20140304 – Contig Integrator for Sequence Assembly
  • CISA has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools
    
    
• Cufflinks 2.2.1 – Transcript Assembler & Abundance Estimator for RNA-Seq
  • Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
    
    
• mapsembler 2.2.4 – Targetted Assembly of Short Sequence Reads
  • Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
    
    
• Tedna 1.2.2 – Transposable Element De Novo Assembler
  • Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.
    
    
• HyDA 1.3.1 / Squeezambler 2.0.3 – Hybrid De Novo Assembler
  • HyDA is a multipurpose assembler, particularly tested for single cell and normal multicell genome co-assembly
    
    
• PANDASEQ 2.8 / Pandaseq-sam 1.3 – PAired-eND Assembler for DNA sequences
  • PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
    
    
• ZORRO 2.2 – Hybrid Sequencing Technology Assembler
  • ZORRO is a hybrid sequencing technology assembler. It merges two sets of pre-assembled contigs into a more contiguous and consistent assembly.
    
    
• FLASH 1.2.11 – Fast Length Adjustment of SHort reads
  • FLASH (Fast Length Adjustment of SHort reads) is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.
    
    
• ALLPATHS-LG 51750 – Whole Genome Shotgun Assembler
  • ALLPATHS-LG (Large Genome) is a whole genome shotgun assembler that can generate high quality assemblies from short reads. It works on both small and large (mammalian size) genomes. To use it, you should first generate ~100 base Illumina reads from two libraries: one from ~180 bp fragments, and one from ~3000 bp fragments, both at about 45x coverage. Sequence from longer fragments will enable longer-range continuity.
    
    
• More Tools at http://bioinformaticsonline.com/pages/view/30440/genome-assembly-tools-and-software-part2

Tools

• Parsnp - Core-genome alignment and analysis
• Gingr - Interactive visualization of alignments, trees and variants
• HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

Address of the bookmark: http://samtools.sourceforge.net/swlist.shtml

Classificier of reads from metagenomic sequencing experiments.

•  Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10(4):1–23,

CoMSA

Compressor of multiple sequence alignments of proteins.

•  Deorowicz, S., Walczyszyn, J., Debudaj-Grabysz, A., CoMSA: compression of protein multiple sequence alignment files, Bioinformatics, 2019; 35(2):22–234,

DSRC

Compressor of sequencing reads.

•  Roguski, L., Deorowicz, S., DSRC 2: Industry-oriented compression of FASTQ files, Bioinformatics, 2014; 30(15):2213–2215,
•  Deorowicz, S., Grabowski, Sz., Compression of DNA sequences in FASTQ format, Bioinformatics, 2011; 27(6):860–862,

FAMSA

Multiple sequence alignment designed for huge families of proteins (even containing hundreds of thousands of sequences).

•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., FAMSA: Fast and accurate multiple sequence alignment of huge protein families, Scientific Reports, 2016; 6(33964):

FaStore

Compressor of FASTQ files.

•  Roguski, L., Ochoa, I., Hernaez, M., Deorowicz, S., FaStore - a space-saving solution for raw sequencing data, Bioinformatics, 2018; 34(16):2748–2756,

FQSqueezer

Experimental high-end compressor of FASTQ files.

•  Deorowicz, S., FQSqueezer: k-mer-based compression of sequencing data, Scientific Reports, 2020; 10(578):

GDC

Compressor of collections of genome sequences.

•  Deorowicz, S., Danek, A., Niemiec, M., GDC 2: Compression of large collections of genomes, Scientific Reports, 2015; 5(11565):1–12,
•  Deorowicz, S., Grabowski, Sz., Robust relative compression of genomes with random access, Bioinformatics, 2011; 27(21):2979–2986,

GTC

Genotype databases compressor with support for fast queries.

•  Danek, A., Deorowicz, S., GTC: how to maintain huge genotype collections in a compressed form, Bioinformatics, 2018; 34(11):1834–1840,

GTShark

Genotypes compressor.

•  Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, Bioinformatics, 2019; 35(22):4791–4793,

KMC

Memory frugal k-mer counter.

•  Kokot, M., Długosz, M., Deorowicz, S., KMC 3: counting and manipulating k -mer statistics, Bioinformatics, 2017; 33(17):2759–2761,
•  Deorowicz, S., Kokot, M., Grabowski, Sz., Debudaj-Grabysz, A., KMC 2: Fast and resource-frugal k-mer counting, Bioinformatics, 2015; 31(10):1569–1576,
•  Deorowicz, S., Debudaj-Grabysz, A., Grabowski, Sz., Disk-based k-mer counting on a PC, BMC Bioinformatics, 2013; 14():Article no. 160,

Kmer-db

Tool for estimation of evolutionary distances in a collection of genomes.

•  Deorowicz, S., Gudys, A., Dlugosz, M., Kokot, M., Danek, A., Kmer-db: instant evolutionary distance estimation, Bioinformatics, 2019; 35(1):133–136,

MuGI

Index allowing queries for a collection of multiple genome sequences.

•  Danek, A., Deorowicz, S., Grabowski, Sz., Indexes of Large Genome Collections on a PC, PLOS ONE, 2014; 9(10):e109384,

ORCOM

Experimental compressor of sequencing reads.

•  Grabowski, Sz., Deorowicz, S., Roguski, L., Disk-based compression of data from genome sequencing, Bioinformatics, 2014; 31(9):1389–1395,

PgSA

Index allowing queries for a collection of sequencing reads.

•  Kowalski, T., Grabowski, Sz., Deorowicz, S., Indexing arbitrary-length k-mers in sequencing reads, PLOS ONE, 2015; 10(7):1–16,

QuickProbs

Multiple sequence alignment designed especially for GPU.

•  Gudys, A., Deorowicz, S., QuickProbs 2: towards rapid construction of high-quality alignments of large protein families, Scientific Reports, 2017; 7(41553):
•  Gudys, A., Deorowicz, S., QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors, PLOS ONE, 2014; 9(2):e88901,

RECKONER

Read error corrector.

•  Maciej Długosz, M., Deorowicz, S., RECKONER: read error corrector based on KMC, Bioinformatics, 2017; 33(7):1086–1089,

TGC

Compressor of collections of genomes given in Variant Call Format (VCF) files.

•  Deorowicz, S., Danek, A., Grabowski, Sz., Genome compression: a novel approach for large collections, Bioinformatics, 2013; 29(20):2572–2578,

VCFShark

Compressor of VCF files.

•  Deorowicz, S., Danek, A., GTShark: Genotype compression in large projects, biorxiv.org, 2020; ():

Whisper

Experimental mapper of whole genome sequencing data.

•  Deorowicz, S., Gudys, A., Whisper 2: indel-sensitive short read mapping, bioRxiv.org, 2019; :
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Whisper: read sorting allows robust robust mapping of DNA sequencing data, Bioinformatics, 2019; 35(12):2043–2050,
•  Deorowicz, S., Debudaj-Grabysz, A., Gudys, A., Grabowski, Sz., Robust mapping of whole genome sequencing data, Poster at The Biology of Genomes Conference, 2017;