CLASS and ASprofile: Resources for Alternative Splicing Annotation from RNA-seq Data

We present two novel software packages for analysis and annotation of alternative splicing from RNA-seq data. The first, CLASS, assembles full-length or partial splice variants from RNA-seq data based on local read coverage patterns, contiguity constraints from read pairs and spliced reads, and optionally information about gene structure extracted from cDNA sequence databases. The algorithmic underpinnings of CLASS are: i) a linear program to infer exons, ii) a compact splice graph representation of a gene and its splice variants, and iii) a transcript selection scheme that takes into account contiguity constraints and, where available, knowledge about gene structure. The second, ASprofile, is a suite of programs for discovering alternative splicing events from transcripts assembled from RNA-seq data and comparing the event profiles across multiple samples or conditions. We illustrate with an analysis of the sixteen tissue Human Body Map RNA-seq data produced and made publicly available by Illumina. Programs can be accessed at http://genomics.jhu.edu/software/ASprofile/. Funding: NSF ABI-1159078.