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.
RNA-Seq; Gene structure; Transcriptomics; Sequence assembly
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
If you find errors, please report here.
SECTIONS
TutorialsFind thousands of Bioinformatics and Life Science software tools and databases in the newly launched
Ads