ChopStitch is a new method for finding putative exons 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 detects base substitutions in transcript sequences corresponding to 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 reported as splice graphs in dot output format.


  • Hamza Khan*, Hamid Mohamadi*, Benjamin P Vandervalk, Rene L Warren, Justin Chu, Inanc Birol; ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing dataBioinformatics, btx839, *Joint First Authors

Current Release

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All Releases

Version Released Description Licenses Status
1.0.0 Jan 05, 2018 Fixing minor bugs. Improving performance. GPLv3 final
0.0.1 Feb 02, 2017 See ChopStitch GitHub page for details. GPLv3 for non-commercial usage
GPLv3 for non-commercial usage
GPLv3 for non-commercial usage
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