When Swarm is chosen for the ITS, the names of the sequences are OtuXX and not ASVXX

[cpavloud]

Hi!

Just a comment for PEMA v.2.1.4, probably it's a small bug.
When Swarm is chosen as a clustering algorithm for ITS, altough the asvs.swarms file is created in the end, the names of the sequences and, subsequently, the names at the extenedFinalTable.tsv and finalTable.tsv are OtuXXX instead of ASVXXX.

[hariszaf]

Hi @cpavloud
Thanks for the issue.
Is this the case only with ITS or with other markers as well?

[cpavloud]

I'm not really sure but I will keep an eye on it.

For COI it's fine.

[JustinePa]

In the ITS output:
finalTable, extendedFinalTable, all_sequences_grouped, allTab_ITS_taxon_assign, and asvs_representative_all_samples use OtuXX, which should not be as they are ASVs.

COI is indeed fine.

[hariszaf]

Thanks @JustinePa for feedback. 🙇