VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.

References:

• Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016 Oct 18;4

• VSEARCH Main Site

• Module Name: vsearch (see the modules page for more information)
• Multithreaded
• Example files in $VSEARCH_EXAMPLES

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load vsearch
[user@cn3144 ~]$ ln -s /usr/local/apps/vsearch/vsearch-data/BioMarKs50k.fsa .
[user@cn3144 ~]$ vsearch --cluster_fast BioMarKs50k.fsa --id 0.97 --centroids vsearch.out

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. vsearch.sh). For example:

#!/bin/bash
module load vsearch
vsearch --usearch_global queries.fsa --db database.fsa --id 0.9 --alnout alnout.txt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] vsearch.sh

Create a swarmfile (e.g. vsearch.swarm). For example:

vsearch --usearch_global queries1.fsa --db database.fsa --id 0.9 --alnout alnout1.txt
vsearch --usearch_global queries2.fsa --db database.fsa --id 0.9 --alnout alnout2.txt
vsearch --usearch_global queries3.fsa --db database.fsa --id 0.9 --alnout alnout3.txt
vsearch --usearch_global queries4.fsa --db database.fsa --id 0.9 --alnout alnout4.txt

Submit this job using the swarm command.

swarm -f vsearch.swarm [-g #] [-t #] --module vsearch