Human removal in QIIME 2?

Developer Discussion
4

Hi @jwdebelius @timanix @colinvwood ,

Yes human read filtering from shotgun metagenome data has been possible in QIIME 2 for a few releases now, as outlined by @gregcaporaso here, and we are working on further updates/improvements and a tutorial. Two approaches/three methods are already available (and combining both approaches is recommended):

  1. read mapping to multiple genome references with bowtie2 (in q2-quality-control) or minimap2
  2. classification of reads with kraken2 against an appropriate database

The issue is not with the methods per se (not that anyone's perfect), but with the reference databases, e.g., using a suitable collection of human reference genomes instead of mapping to a single reference genome :stuck_out_tongue: .

We will have further updates and info on this in the near future!

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