Replace USEARCH with VSEARCH ( result so far - vsearch: unrecognized option '-cluster_otus' )

[JustGitting]

Hi,

I tried to substitute USEARCH with VSEARCH by setting the following parameter in the tornado-params.sh file:

#Name of the usearch version 7 binary. Could be the actual name,
#or some other name. It needs to be in the PATH
# USEARCH7=usearch7
USEARCH7=vsearch

However, I get the following error when executing the tornado_run_pipeline.sh

Reading file test_R2.derep.fasta 100%
334108789 nt in 1679893 seqs, min 187, max 200, avg 199
Getting sizes 100%
Sorting 100%
Median abundance: 3
Writing output 100%
vsearch v2.0.0_linux_x86_64, 94.4GB RAM, 24 cores
https://github.com/torognes/vsearch

Reading file test_paired.derep.fasta 100%
1252200975 nt in 2822165 seqs, min 374, max 450, avg 444
Getting sizes 100%
Sorting 100%
Median abundance: 3
Writing output 100%
**vsearch: unrecognized option '-cluster_otus'**

I've searched VSEARCH's documentation, but it would appear to lack the OTU clustering function of USEARCH.

I would be keen to remove the dependency of USEARCH in place of VSEARCH because we can check and improve the source code of the later.

In the mean time, is it possible to turn off the "-cluster_otus" option until VSEARCH implements the function?

Thanks

[JustGitting]

Unfortunately, VSEARCH does not support the _clusterotus functionality...yet.

[colinbrislawn]

Looks like vsearch support only extends to the --derep_fulllength command. https://github.com/pjeraldo/imtornado2/commit/3faaa712dfda51f70df8fd1c125c4f6ce87f15af#diff-41b175b7529bf026a4e17a10d957fa26R102

👍 for vsearch support! It is an excellent piece of open source science software (and the devs are nice).