This article is part of the supplement: Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013)
CLASS: constrained transcript assembly of RNA-seq reads
1 Department of Computer Science, Johns Hopkins University, Baltimore, MA 21218, USA
2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MA 21205, USA
BMC Bioinformatics 2013, 14(Suppl 5):S14 doi:10.1186/1471-2105-14-S5-S14Published: 10 April 2013
RNA-seq has revolutionized our ability to survey the cellular transcriptome in great detail. However, while several approaches have been developed, the problem of assembling the short reads into full-length transcripts remains challenging.
We developed a novel algorithm and software tool, CLASS (
In comparisons against leading transcript assembly programs, CLASS is more accurate on both simulated and real reads and produces results that are easier to interpret when applied to large scale real data, and therefore is a promising analysis tool for next generation sequencing data.