Jan 5, 2018

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

Hamza KhanInanc Birol


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. 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 also accounts for base substitutions in transcript sequences that may be derived from sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are represented as splice graphs in DOT output format. ChopStitch is written in Python and C++ and is released under the GPL l...Continue Reading

  • References23
  • Citations


  • This paper may not have been cited yet.

Mentioned in this Paper

Nested Transcripts
DOT-1.1 protein, C elegans
Whole-Genome Shotgun Sequencing
Sequence Determinations, RNA
Nucleic Acid Sequencing
Computer Programs and Programming

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.