BOL: Related items

BRIG

Jit — Thu, 16 Feb 2017 13:14:25 -0600

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page:http://sourceforge.net/tracker/?group_id=328245.

Features:

Images show similarity between a central reference sequence and other sequences as concentric rings.
BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

Address of the bookmark: http://brig.sourceforge.net/

Cgaln

Jit — Wed, 22 Feb 2017 05:14:15 -0600

Cgaln (Coarse grained alignment) is a program designed to align a pair of whole genomic sequences of not only bacteria but also entire chromosomes of vertebrates on a nominal desktop computer. Cgaln performs an alignment job in two steps, at the block level and then at the nucleotide level. The former "coarse-grained" alignment can explore genomic rearrangements and reduce the regions to be analyzed in the next step. The latter is devoted to detailed alignment within the limited regions found in the first stage. The output of Cgaln is 'glocal' in the sense that rearrangements are taken into consideration while each alignable region is extended as long as possible. Thus, Cgaln is not only fast and memory-efficient, but also can filter noisy outputs without missing the most important homologous segment pairs.

http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/

Address of the bookmark: http://www.iam.u-tokyo.ac.jp/chromosomeinformatics/rnakato/cgaln/

FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads

Jit — Mon, 27 Feb 2017 09:49:45 -0600

FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Address of the bookmark: http://kakitone.github.io/finishingTool/

CLgenomics

Radha Agarkar — Fri, 03 Mar 2017 09:57:28 -0600

CLgenomics is a standalone desktop software specifically designed for bacterial genome analysis. This program has a powerful multi-genome browser, which enables rapid and responsive exploration of bacterial genomes.

To use CLgenomics, individual genome data (genome sequences + annotation details) are compiled and saved in a specially formatted file called CLG (ChunLab Genomics). Each CLG file corresponds with one bacterial genome. If multiple genomes are being considered and compared, multiple CLG files are needed. ChunLab offers >40,000 CLG files of publicly available Bacterial and Archaeal genomes.

Address of the bookmark: https://chunlab.wordpress.com/clgenomics-software/

CONCOCT: Clustering cONtigs with COverage and ComposiTion

Jit — Mon, 06 Mar 2017 04:08:16 -0600

A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

Warning! This software is to be considered under development. Functionality and the user interface may still change significantly from one version to another. If you want to use this software, please stay up to date with the list of known issues:https://github.com/BinPro/CONCOCT/issues

Address of the bookmark: https://github.com/BinPro/CONCOCT

SeqMule: Automated human exome/genome variants detection

Abhimanyu Singh — Tue, 07 Mar 2017 10:12:36 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

DeCoSTAR - Detection of Co-evolution

Jit — Fri, 14 Apr 2017 06:27:25 -0500

DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.
Ancestral genes or domains are deduced from reconciled gene trees in a context of birth, speciation, duplication, loss, transfer, which are either given as input or computed with the ecceTERA package, to which DeCoSTAR is integrated. DeCoSTAR constructs parsimonious scenarios of gains and breakages of adjacencies, and contains in particular all the features of previous software DeCo, DeCoLT, ArtDeCo and DeClone. It provides statistical supports on ancestral adjacencies, or the possibility to handle badly assembled genomes.
DeCoSTAR is able to reconstruct the histories of domains inside genes, including gene fusion and fission events, as well as ancestral genome structures for dozens of whole genomes from all kingdoms of life in a few minutes.

Address of the bookmark: http://pbil.univ-lyon1.fr/software/DeCoSTAR/

CABOG: Celera Assembler with Best Overlap Graph

Abhimanyu Singh — Mon, 15 May 2017 05:04:39 -0500

CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as mammalian. CABOG is an extension of the Celera Assembler software that was originally developed at Celera for the 2001 publication of the first draft human genome sequence. The software was released to the public domain in 2004. Its open source repository on Source Forge is an internet resource for scientists around the world.

CABOG is one of many software programs called genome assemblers. These programs exist to overcome the fundamental limitation of all sequencing machines, namely, that they read out very few DNA letters at a time. These programs reconstruct genomes that are billions of letters long from the hundreds of letters per read that modern sequencers provide. What these programs do is often described as a scaled up version of a family solving a jigsaw puzzle.

The CABOG software was the first to accomplish many scientific goals. It was the first to assemble the genome of a multicellular organism (Drosophila melanogaster, 2000). It was the first to assemble both parental haplotypes of one human genome (J. Craig Venter, 2007). It was the first to assemble environmental sequence from the oceans (Sargasso Sea in 2004 and Global Ocean Sampling in 2007). It was first to combine reads from first-generation Sanger sequencing machines and second-generation pyrosequencing machines (Marine microbes, 2006). Today, CABOG is one of the leading assembly programs for data sets that include paired end data from the Roche 454 line of sequencing machines.

Address of the bookmark: http://www.jcvi.org/cms/research/projects/cabog/overview/

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

Jit — Tue, 07 Nov 2017 04:36:10 -0600

We describe a new algorithm, meraculous, 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. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ∼280 bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087/

MeDuSa: a multi-draft based scaffolder

Abhimanyu Singh — Wed, 14 Feb 2018 02:49:00 -0600

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries.

Address of the bookmark: https://github.com/combogenomics/medusa