Tree building from post deblur files


I downloaded and merged a few deblurred biom tables from qiita and want to build a tree in QIIME2.
The deblur was done without hashes, while the rep-seqs comes from hashes (currently the repseqs are in the biom table). Is there a workaround to create a repseqs file?


Hi @myor,

This is a similar question than:

However, some of the steps in Qiita have changed and I think having a shorter answer here is worth it. Anyway, the biggest difference is that we shouldn’t have the lower/upper case issue not present anymore so we just need to run:

biom summarize-table --observations -i your_biom.biom \
    | tail -n +16 | awk -F ':' '{print ">"$1"\n"$1}' > rep_seqs.fna

Then import your biom and fna to QIIME2 using the regular import commands.

Hope this helps.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.