ASVs from dada2?

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Hello!

I’m relatively new to microbiome work and I have a quick question regarding ASVs :slight_smile:
If I’m using the dada2 pipeline in the ‘Moving Pictures’ tutorial (“Moving Pictures” tutorial — QIIME 2 2021.2.0 documentation), are the rep-seqs.qzv sequences ASVs or are they OTUs?
If they are ASVs, is there an easy way to rename these sequences to e.g. ASV1, ASV2, 3ASV etc or do they have to be named e.g. 595da10b1f9b9e19217c45da758d7e75 forever? :face_with_monocle:

Any tips would be greatly appreciated! :smiley:
Thanks :partying_face:

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Hello there!
If you are using Dada2 or Deblur, you will obtain ASVs.
There is no plugin in Qiime2 to rename ASVs. If you will manage to do so outside of Qiime2, you also should rename sequences in rep-seq.qza file.
Also, ASV names are unique for the sequence, and the same sequences from different studies will have the same name.

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Brill, thank you very much for this info, I didn’t know the names are unique to these sequences which is very interesting! :smiley:

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Like @timanix said, @simonhb, those long gross feature IDs are sequence-unique, because they are hashes of the sequence themselves. You can turn this setting off with q2-dada2's -p-hashed-feature-ids parameter, but the value of having a unique ID that is tied to the sequence itself generally outweighs readability concerns. These properties:

  • prevent accidental confusion or cognitive bias caused by “meaningful” user-generated IDs
  • allow straightforward comparison of ids across runs (you can compare IDs rather than full-length sequences)
  • allow you to merge feature tables across multiple sequence runs (if you use the same DADA2 parameters for all runs)

It is possible to rename-ids in QIIME 2 feature tables, though I don’t think there’s a similar tool for FeatureData[Sequence] objects like your representative seqs at this time. I haven’t used this myself, but I suspect it would let you assign human-readable IDs to features or samples prior to visualization, which could save you time editing figures.

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