Jun 17, 2009

De novo transcriptome assembly with ABySS

Bioinformatics
Inanç BirolSteven J M Jones

Abstract

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. 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. 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. ibirol@bcgsc.ca.

  • References21
  • Citations204

References

  • References21
  • Citations204

Citations

Mentioned in this Paper

Metabolic Process, Cellular
Genome
Tumor Tissue Sample
Gene Expression
Computer Programs and Programming
Lymphoma, Follicular
Sequence Determinations, DNA
Base Pairing
Transcriptome
Shotgun Sequencing

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