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Trans-ABySS

Trans-ABySS

Trans-ABySS is a tool for de novo transcriptome assembly using short reads. The Trans-ABySS algorithm specifically addresses issues caused by local coverage variations by first computing assemblies of substrings using various stringencies. It then merges the separate assemblies into contigs. It can handle paired-end reads, multiple insert sizes, but not strandedness. This tool requires ABySS and BLAT.

Topic

RNA-Seq; Gene structure; Transcriptomics; Sequence assembly

Details

  • Operation: Transcriptome assembly; De-novo assembly
  • Input: FASTQ; FASTA; SAM; QSEQ; BAM
  • Output: FASTA
  • Software interface: Command-line user interface
  • Language: Python;AWK
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: -
  • Maturity: Mature
  • Credit: Genome Canada, Genome British Columbia, Michael Smith Foundation for Health Research, the Canadian Institute of Health Research (CIHR), the CIHR Bioinformatics Training Program for Health Research.
  • Contact: Ka Ming Nip kmnip _at_ bcgsc.ca | Readman Chiu rchiu _at_ bcgsc.ca
  • Collection: -

Publications

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. https://doi.org/10.1038/nmeth.1517
PMID: 20935650


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