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dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.
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Add alignment post-processing for stage2. #164

Closed ctb closed 3 years ago

ctb commented 3 years ago

This PR adds alignment post-processing to the stage2 workflow.

This is the section of the workflow to mashmap/nucmer alignments into specific recommendations for contig removal, + provide all the necessary information for reporting/output.