BOL: Related items

A 3D Map of the Human Genome

Fri, 12 Dec 2014 22:27:55 -0600

Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell.

n50PlottingTools

Jit — Mon, 08 Feb 2016 15:39:04 -0600

Tools to create plots showing N-statistics for genome assemblies

More at https://github.com/dentearl/n50PlottingTools

Address of the bookmark: https://github.com/dentearl/n50PlottingTools

Easyfig

Poonam Mahapatra — Fri, 29 Apr 2016 05:49:39 -0500

Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig. Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

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

RACA: Reference-Assisted Chromosome Assembly

Priya Singh — Wed, 06 Apr 2016 09:29:50 -0500

Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads.

http://www.ncbi.nlm.nih.gov/pubmed/23307812

http://bioen-compbio.bioen.illinois.edu/RACA/

Address of the bookmark: http://bioen-compbio.bioen.illinois.edu/RACA/

Trimmomatic: A flexible read trimming tool for Illumina NGS data

Jit — Fri, 15 Apr 2016 05:58:53 -0500

Paired End:

java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This will perform the following:

Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
Remove leading low quality or N bases (below quality 3) (LEADING:3)
Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
Drop reads below the 36 bases long (MINLEN:36)

More at http://www.usadellab.org/cms/?page=trimmomatic

Address of the bookmark: http://www.usadellab.org/cms/?page=trimmomatic

ALE: a Generic Assembly Likelihood Evaluation Framework for Assessing the Accuracy of Genome and Metagenome Assemblies

Neel — Tue, 26 Apr 2016 03:38:43 -0500

Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment and k-mer frequency. ALE pinpoints synthetic errors in both single and metagenomic assemblies, including single-base errors, insertions/deletions, genome rearrangements and chimeric assemblies presented in metagenomes. At the genome level with real-world data, ALE identifies three large misassemblies from the Spirochaeta smaragdinae finished genome, which were all independently validated by Pacific Biosciences sequencing. At the single-base level with Illumina data, ALE recovers 215 of 222 (97%) single nucleotide variants in a training set from a GC-rich Rhodobacter sphaeroides genome. Using real Pacific Biosciences data, ALE identifies 12 of 12 synthetic errors in a Lambda Phage genome, surpassing even Pacific Biosciences' own variant caller, EviCons. In summary, the ALE framework provides a comprehensive, reference-independent and statistically rigorous measure of single genome and metagenome assembly accuracy, which can be used to identify misassemblies or to optimize the assembly process.

More at http://www.ncbi.nlm.nih.gov/pubmed/23303509

Address of the bookmark: http://sc932.github.io/ALE/about.html

MEDEA: Comparative Genomic Visualization with Adobe Flash

Jit — Tue, 26 Apr 2016 12:15:16 -0500

As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets.

More at http://www.broadinstitute.org/annotation/medea/

Address of the bookmark: http://www.broadinstitute.org/annotation/medea/

Fancy Oneliner for Bioinformatics !!

Poonam Mahapatra — Thu, 07 Jul 2016 12:05:50 -0500

This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder structures as we have. We are sharing these codes with the intention that if they are useful and help you in your analyses, then we will be appropriately credited as considerable effort has been put into devising them.

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html

ART: Set of Simulation Tools

Jit — Thu, 03 Nov 2016 08:28:25 -0500

ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. VarSim) for evaluating variant calling tools or methods.

Address of the bookmark: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

BIMA V3: an aligner customized for mate pair library sequencing

Abhimanyu Singh — Wed, 14 Dec 2016 15:20:00 -0600

Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a challenging and
time consuming process for most NGS alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.), and presence of structural variant breakpoints within reads increases mapping and alignment complexity. We describe an algorithm that is up to 20 times faster and 25% more accurate than popular NGS alignment programs when processing mate pair sequencing.
Availability: http://bioinformaticstools.mayo.edu/research/bima/
Contact: vasmatzis.george@mayo.edu

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2014/02/12/bioinformatics.btu078.full.pdf