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