Start Over

De novo transcriptome assembly with ABySS.

Authors :: Birol I
Jackman SD
Nielsen CB
Qian JQ
Varhol R
Stazyk G
Morin RD
Zhao Y
Hirst M
Schein JE
Horsman DE
Connors JM
Gascoyne RD
Marra MA
Jones SJ
Source :: Bioinformatics (Oxford, England) [Bioinformatics] 2009 Nov 01; Vol. 25 (21), pp. 2872-7. Date of Electronic Publication: 2009 Jun 15.
Publication Year :: 2009
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.<br />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 approximately 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.<br />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.<br />Contact: ibirol@bcgsc.ca.