ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

ABSTRACT:

Motivation

Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques, when the species and closely related species lack high quality reference resources. For certain applications such as de novo annotation, information on putative exons and alternative splicing may be desirable.

Results

Here we present ChopStitch, a new method for finding putative exons de novo and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-Seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm a

SUBMITTER: Khan H 

PROVIDER: S-EPMC5946899 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature