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De novo transcriptome assembly with ABySS
Open accessAbstract
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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Computational methods for transcriptome annotation and quantification using RNA-seq
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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
- OpenAlex
- W2112491476
- Cited by
- 400
- References
- 3
- FWCI
- 14.76
- Type
- journal article
- Language
- en
- Open access
- bronze
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- 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. (2009). De novo transcriptome assembly with ABySS. Bioinformatics. https://doi.org/10.1093/bioinformatics/btp367
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