Pairoscope (formerly Yenta) was developed as a quick and simple way to generate diagrams indicating the relationship of paired end sequencing reads. It functions by displaying multiple genomic regions, their read depth at each base in the region and arcs within or between regions to indicate pairing information. Currently, Pairoscope supports the graphing of multiple regions, but they must be at different locations: the behavior of Pairoscope is undefined if attempting to graph the same region twice. It uses a bam file as input, and color codes the read pair graph to reflect different types of abnormally oriented reads. Individual reads are represented as vertical lines drawn at the genomic location where the read mapped.
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