Title

De novo assembly and analysis of RNA-seq data.

Authors

Robertson, Gordon; Schein, Jacqueline; Chiu, Readman; Corbett, Richard; Field, Matthew; Jackman, Shaun D.; Mungall, Karen; Sam Lee; Okada, Hisanaga Mark; Qian, Jenny Q.; Griffith, Malachi; Raymond, Anthony; Thiessen, Nina; Cezard, Timothee; Butterfield, Yaron S.; Newsome, Richard; Chan, Simon K.; Rong She; Varhol, Richard; Kamoh, Baljit

Abstract

We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.

Subjects

RNA; GENETIC transcription; GENOMICS; GENETIC code; LABORATORY mice

Publication

Nature Methods, 2010, Vol 7, Issue 11, p909

ISSN

1548-7091

Publication type

Academic Journal

DOI

10.1038/nmeth.1517