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Cited by 400

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

De novo transcriptome assembly with ABySS

Open access
Birol, Inanç, Jackman, Shaun D., Nielsen, Cydney B., Qian, Jenny Q., Varhol, Richard, Stazyk, Greg, Morin, Ryan D., Zhao, Yongjun, Hirst, Martin, Schein, Jacqueline E., Horsman, Doug E., Connors, Joseph M., Gascoyne, Randy D., Marra, Marco A., Jones, Steven J. M.·2009·Bioinformatics
DOI 10.1093/bioinformatics/btp367
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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. 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@bcgsc.ca

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Citations

Cites

Research works printed but not linked: 22

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Metadata

Authors
Birol, I., Jackman, S. D., Nielsen, C. B., Qian, J. Q., Varhol, R., Stazyk, G., Morin, R. D., Zhao, Y., Hirst, M., Schein, J. E., Horsman, D. E., Connors, J. M., Gascoyne, R. D., Marra, M. A., & Jones, S. J. M.
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2009-06-15
Volume
25
Issue
21
Pages
2872-2877
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btp367
OpenAlex
W2112491476
Cited by
400
References
3
FWCI
14.76
Type
journal article
Language
en
Open access
bronze

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