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Bioinformatics Advance Access originally published online on June 15, 2009
Bioinformatics 2009 25(21):2872-2877; doi:10.1093/bioinformatics/btp367
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

De novo transcriptome assembly with ABySS

Inanç Birol 1,*, Shaun D. Jackman 1, Cydney B. Nielsen 1, Jenny Q. Qian 1, Richard Varhol 1, Greg Stazyk 1, Ryan D. Morin 1, Yongjun Zhao 1, Martin Hirst 1, Jacqueline E. Schein 1, Doug E. Horsman 2, Joseph M. Connors 2, Randy D. Gascoyne 2, Marco A. Marra 1 and Steven J. M. Jones 1

1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada

* To whom correspondence should be addressed.


  Abstract

Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable.

Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled ~194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1% of the genome.

Availability and Implementation: Source code and binaries of ABySS are freely available for download at http://www.bcgsc.ca/platform/bioinfo/software/abyss. Assembler tool is implemented in C++. The parallel version uses Open MPI. ABySS-Explorer tool is implemented in Java using the Java universal network/graph framework.

Contact: ibirol{at}bcgsc.ca

Associate Editor: Alex Bateman

Received on April 27, 2009; revised on June 5, 2009; accepted on June 9, 2009

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