Figure 3

PathoMap module workflow. The PathoMap module aligns reads to the target library and removes any sequences that align to the filter library. PathoMap will: (1) index the reference library; (2) align the reads to the target library; and (3) filter any of the target-matching reads that also match the filter library. The current version of PathoMap includes a Bowtie 2 wrapper and allows users can conduct any part of the alignments outside the PathoMap framework.