De novo assembly and analysis of RNA-seq data

Robertson, Gordon, Schein, Jacqueline, Chiu, Readman, Corbett, Richard, Field, Matthew, Jackman, Shaun D., Mungall, Karen, Lee, Sam, Okada, Hisanaga Mark, Qian, Jenny Q., Griffith, Malachi, Raymond, Anthony, Thiessen, Nina, Cezard, Timothee, Butterfield, Yaron S., Newsome, Richard, Chan, Simon K., She, Rong, Varhol, Richard, Kamoh, Baljit, Prabhu, Anna-Liisa, Tam, Angela, Zhao, YongJun, Moore, Richard A., Hirst, Martin, Marra, Marco A,, Jones, Steven J.M., Hoodless, Pamela A., and Birol, Inanc (2010) De novo assembly and analysis of RNA-seq data. Nature Methods, 7 (11). pp. 909-912.

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View at Publisher Website: http://dx.doi.org/10.1038/nmeth.1517
 
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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.

Item ID: 43193
Item Type: Article (Refereed Research - C1)
ISSN: 1548-7105
Funders: Genome Canada (GC), Genome British Columbia (GBC), Michael Smith Foundation for Health Research (MSFHR), Canadian Institute of Health Research
Date Deposited: 25 Oct 2016 23:21
FoR Codes: 06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060102 Bioinformatics @ 25%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 25%
08 INFORMATION AND COMPUTING SCIENCES > 0803 Computer Software > 080301 Bioinformatics Software @ 50%
SEO Codes: 89 INFORMATION AND COMMUNICATION SERVICES > 8902 Computer Software and Services > 890299 Computer Software and Services not elsewhere classified @ 100%
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