Tag: ABySS

ABySS 2.3.2 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.3.2

:: DESCRIPTION

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.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: MORE INFORMATION

Citation

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.
Sealer: a scalable gap-closing application for finishing draft genomes.
BMC Bioinformatics. 2015 Jul 25;16(1):230. doi: 10.1186/s12859-015-0663-4. PMID: 26209068; PMCID: PMC4515008.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.
Konnector v2.0: pseudo-long reads from paired-end sequencing data.
BMC Med Genomics. 2015;8 Suppl 3(Suppl 3):S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23. PMID: 26399504; PMCID: PMC4582294.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123

Trans-ABySS 2.0.1 – Analyze ABySS multi-k-assembled Shotgun Transcriptome Data.

Trans-ABySS 2.0.1

:: DESCRIPTION

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.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Trans-ABySS

:: MORE INFORMATION

Citation

Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I.
De novo assembly and analysis of RNA-seq data.
Nat Methods. 2010 Nov;7(11):909-12. Epub 2010 Oct 10.

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