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broadinstitute / viral-classify

viral-ngs: taxonomic identification, classification, and filtering steps
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filter bam from taxa #16

Closed dpark01 closed 4 years ago

dpark01 commented 4 years ago
  1. adds an --exclude option to filter_bam_to_taxa to make it work in the opposite direction
  2. changes the picard samtofastq prior to kraken2 to dump to an uncompressed fastq (no gz) for speed's sake