Guidance modifying q2-vsearch to recover UC file

Hi everyone,

I would like to contribute to qiime2 by modifying the q2-vsearch plugin to optionally retain the "UC" file output. As Nicholas, Colin and I previously discussed (original post), the "UC" file is lost upon completion of clustering because it is opened as a tmp file that gets automatically deleted. Since the UC file contains information about who is in each cluster, it could be quite useful to retain, e.g. if one wanted to compare distributional patterns between OTUs and their constituent ASVs.

I think it should be pretty simple to solve this based on our previous discussion. Should I just fork the github repo, test, and make a pull request once I think it's solved?

Any guidance you can offer about best practices or suggested strategies would be really appreciated!



Hi @jcmcnch, responding to this post in detail is on my radar, but I probably won’t get to it until next week. Stay tuned!

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Hey @jcmcnch! Thanks so much for your patience, things have been pretty busy here at Q2HQ!

Awesome! We would love your support!

Unfortunately QIIME 2 doesn't currently support "optional" outputs (it is on our radar, though). If you are going to add the UC file as an output, it would need to always be included. I don't personally see an issue with this, though.

This does sound pretty handy!

Start here:

In particular, check out the sections on:

As well, here is a PR that adds a few new formats and semantic types, that might serve as a useful reference: ENH: Multiplexed sequences by thermokarst · Pull Request #163 · qiime2/q2-types · GitHub

Please keep us posted - if you run into any hiccups or issues we are here to help. Thanks so much!


An off-topic reply has been merged into an existing topic: vsearch de novo output --uc option

Please keep replies on-topic in the future.