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De novo transcriptome assembly with ABySS

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Open access via publisher
Authors
Birol, I.
Jackman, S.
Nielsen, C.
Qian, J.
Varhol, Richard
Stazyk, G.
Morin, R.
Zhao, Y.
Hirst, M.
Schein, J.
Horsman, D.
Connors, J.
Gascoyne, R.
Marra, M.
Jones, S.
Date
2009
Type
Journal Article

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Citation
Birol, I. and Jackman, S. and Nielsen, C. and Qian, J. and Varhol, R. and Stazyk, G. and Morin, R. et al. 2009. De novo transcriptome assembly with ABySS. Bioinformatics. 25 (21): pp. 2872-2877.
Source Title
Bioinformatics
DOI
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Department of Health Policy and Management
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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. © The Author 2009. Published by Oxford University Press. All rights reserved.