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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 paired-reads alignments in SAM or BAM format and single-end reads 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).
DiscoPlot of a mock genome. A mock genome was created by adding genomic rearrangements to the chromosome of E. coli str. UTI89. Paired-end reads generated from the mock genome (query) with GemSim and mapped back to UTI89 (reference). The first ~500 Kbp were then visualised using DiscoPlot.