Trans-ABySS | Tool name | Trans-ABySS |
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| URL | http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss |
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| Important features | 1. Designed to analyze ABySS-assembled whole-genome shotgun transcriptome data. Contains scripts that will map assembled contigs to known transcripts, deduce novel splicing events such as exon-skipping, novel exons, intron retention, novel introns, and alternative splicing.
2. Also contains scripts that will extract potential SNVs, INDELs, and gene-fusion events from alignment data. |
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| Citations | 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. PubMed PMID: 20935650. |
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| Year of publication | 2010 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | RNA seq alignment |
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| Category | Downloadable |
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| License |
BCCA |
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| Status | |
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| Input file format | Fasta, ABySS k-assemblies |
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| Output file format | |
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| Operating system |
any POSIX-compliant platform |
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| Operating language |
Python and Perl |
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| Platform | Illumina/Solexa |
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| Maintained by | Canada's Michael Smith Genome Sciences Centre
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| Downloadable file format | |
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| Submission file format | |
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