separate archaea-only database from Silva database

HI @Susun,

Who recommended this? This sounds an awful lot like this recent conversation, which you can read for more details. In my opinion, making an archaea-only database might not be explicitly wrong but it could really open up a new set of unintended issues so you should be careful if you want to do this. See this conversation:

Don't use matlab... looks like it is mangling the format and inserting special characters. Probably an easy fix, but there are easier fixes:

qiime taxa filter-seqs would do what you need, you can see the documentation for more usage details.

You might also need to trim the taxonomy file as well, to match the filtered sequence file. We have a tool for that as well, but it is not part of the QIIME 2 2020.11 standard release and needs to be installed separately:

if you install and use that, the method you want is called "filter-taxa", use like so:

qiime rescript filter-taxa --i-taxonomy taxa.qza --m-ids-to-keep-file filtered-sequences.qza --o-filtered-taxonomy filtered-taxonomy.qza

Good luck!

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