DiscoPlot: Discordant read visualisation
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics, Microbiology
- Keywords
- Bioinformatics, software, structural variation, misalignment, microbial genomics
- Copyright
- © 2015 Sullivan et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- (2015) DiscoPlot: Discordant read visualisation. PeerJ PrePrints 3:e1038v1 https://doi.org/10.7287/peerj.preprints.1038v1
Abstract
Over the last decade, the emergence of high-throughput sequencing has led to an increase in both the size and scope of genome sequencing projects. Although genome sequencing and analysis has changed dramatically during this time, the way read alignments are visualised has remained largely unchanged. To address the problem of visualising growing sequencing datasets, we have developed DiscoPlot, a tool for visualising read alignments using a two-dimensional scatterplot. DiscoPlot allows the user to quickly identify genomic rearrangements, misassemblies and sequencing artefacts by providing a scalable method for visualising large sections of the genome. It reads single-end or paired read alignments in SAM, BAM or standard BLAST tab format and creates a scatter plot of opaque crosses representing the alignments to a reference. DiscoPlot is freely available (under a GPL license) for download (Mac OS X, Unix and Windows) at https://mjsull.github.io/DiscoPlot.
Author Comment
This is Version 1 of the manuscript, formatted for PeerJ Submission.