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Publications of the Week

ChopStitch: Exon Annotation and Splice Graph Construction Using Transcriptome Assembly and Whole Genome Sequencing Data

By January 19, 2018No Comments

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 This week we profile a recent publication in Bioinformatics from Dr. Inanc Birol  (fourth from left)
and Hamza Khan (sixth from left) at the Michael Smith Genome Sciences Centre.

Can you provide a brief overview of your lab’s current research focus?

We at the Bioinformatics Technology lab of BC Genome Sciences Centre, analyze high-throughput sequencing data to study genomes and transcriptomes of model, non-model organisms, and humans. We are working on developing bioinformatics tools and algorithms for de novo sequence assembly, sequence alignment, biological data analysis and visualization, while using the latest NGS technologies such as Chromium linked reads from 10x Genomics and long reads from Oxford Nanopore Technology instruments.

What is the significance of the findings in this publication?

ChopStitch is a de novo annotation tool that can find putative exons and construct splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS). It can annotate de novo transcriptome assemblies, find novel-exons in coding as well as non-coding mRNA transcripts, and search alternative mRNA splicing events in non-model organisms, thus exploring new loci for functional analysis and studying genes that were previously inaccessible.

What are the next steps for this research?

The next steps would involve using this tool for many of our sequencing projects and looking into ways of customising ChopStitch for a range of different plant and animal species. We also encourage the scientific community to use ChopStitch and provide relevant feedback, which would help us in due course.

This research was funded by:

We thank Genome Canada, Genome BC, and British Columbia Cancer Foundation for their financial support. The work is also partially funded by the National Institutes of Health under Award Number R01HG007182. The content of this work is solely the responsibility of the authors, and does not necessarily represent the official views of the National Institutes of Health or other funding organizations.

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