Chimera detecting in vsearch OTU clustering

[jk.c...@gmail.com]

Hello,

In the usearch program, it suggests not generally doing any additional chimera detection:

"The chimera filter in cluster_otus is very effective, so I generally don't do any additional filtering. It may be possible to find some additional chimeras by running uchime2_ref on the OTU sequences generated by cluster_otus. You should use ‑mode high_confidence to reduce the risk of false positives." - UPARSE pipeline instructions online.

Since (to my knowledge) there isn't an identical cluster_otus program (instead there seems to be --cluster_fast, --cluster_size or --cluster_smallmem) is the clustering function in vsearch the same? Are additional chimera detection steps also not generally recommended for vsearch?

Thanks,
Julia

[Torbjørn Rognes]

The cluster_otus command in USEARCH performs clustering and chimera detection simultaneously. VSEARCH does not include the cluster_otus command. The cluster_fast, cluster_size and cluster_smallmem commands in VSEARCH performs clustering only. It is therefore highly recommended to perform chimera detection with uchime_denovo or uchime_ref using VSEARCH.

- Torbjørn