Chimera detecting in vsearch OTU clustering

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Jan 6, 2017, 11:47:18 AM1/6/17
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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?


Torbjørn Rognes

Jan 6, 2017, 12:15:17 PM1/6/17
to VSEARCH Forum
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
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