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Xenomapper: Mapping reads in a mixed species context

Xenomapper is a utility for post processing mapped DNA sequencing reads that have been aligned to a primary genome and a secondary genome, and binning reads into species specific, multimapping in each species, unmapped and unassigned categories. It can be used on single end or paired end sequencing data across a wide range of genomics methods including RNAseq. In paired end data evidence of sequence specificity for either read will be used to assign both reads.