Tree building from post deblur files

Hi

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?

Thanks
Michael

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.

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