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2. De novo assembly and analysis of RNA-seq data

Author

Malachi Griffith, Karen Mungall, Steven J.M. Jones, Richard A. Moore, Rong She, Marco A. Marra, Shaun D. Jackman, Yaron S. Butterfield, Richard Newsome, Pamela A. Hoodless, Yongjun Zhao, Richard Corbett, Angela Tam, Hisanaga Mark Okada, Martin Hirst, Timothee Cezard, Inanc Birol, Baljit Kamoh, Richard Varhol, Anna Liisa Prabhu, Simon K. Chan, Gordon Robertson, Readman Chiu, Matthew A. Field, Jenny Q. Qian, Nina Thiessen, Anthony Raymond, Jacqueline E. Schein, and Sam Lee

Subjects
Genetics, Contig, Sequence analysis, Base pair, Gene Expression Profiling, De novo transcriptome assembly, Sequence assembly, Computational Biology, RNA-Seq, Cell Biology, Sequence Analysis, DNA, Biology, Biochemistry, Transcriptome, Mice, Animals, Genomic library, Molecular Biology, Biotechnology
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.

Published
2010

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