De Novo Assembly and Analysis of RNA-seq Data

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2010 Oct 12

PMID 20935650

Citations 465

Authors

Gordon Robertson

Jacqueline Schein

Readman Chiu

Richard Corbett

Matthew Field

Shaun D Jackman

Karen Mungall

Sam Lee

Hisanaga Mark Okada

Jenny Q Qian

Malachi Griffith

Anthony Raymond

Nina Thiessen

Timothee Cezard

Yaron S Butterfield

Richard Newsome

Simon K Chan

Rong She

Richard Varhol

Baljit Kamoh

Anna-Liisa Prabhu

Angela Tam

Yongjun Zhao

Richard A Moore

Martin Hirst

Marco A Marra

Steven J M Jones

Pamela A Hoodless

Inanc Birol

Affiliations

Soon will be listed here.

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.

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