Estimation of alternative splicing isoform frequencies from RNA-Seq data
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Isolasso: a lasso regression approach to RNA-seq based transcriptome assembly
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
T-IDBA: a de novo iterative de bruijn graph assembler for transcriptome
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
FinIS: improved in silico finishing using an exact quadratic programming formulation
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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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