De novo transcriptome assembly with ABySS.
BACKGROUND
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 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.


METHODS
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.


BACKGROUND
ibirol@bcgsc.ca.
Birol
Inanç
I
Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada. ibirol@bcgsc.ca
Jackman
Shaun D
SD
Nielsen
Cydney B
CB
Qian
Jenny Q
JQ
Varhol
Richard
R
Stazyk
Greg
G
Morin
Ryan D
RD
Zhao
Yongjun
Y
Hirst
Martin
M
Schein
Jacqueline E
JE
Horsman
Doug E
DE
Connors
Joseph M
JM
Gascoyne
Randy D
RD
Marra
Marco A
MA
Jones
Steven J M
SJ
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D016678:Genome; D017422:Sequence Analysis, DNA; D012984:Software