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, please set --threads option
• Example files in $VSEARCH_EXAMPLES

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

[user@biowulf ~]$ sinteractive --mem=4G --gres=lscratch:5
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 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 46116226]$ cp $VSEARCH_EXAMPLES BioMarKs50k.fsa .
[user@cn3144 46116226]$ vsearch --threads 2 --cluster_fast BioMarKs50k.fsa --id 0.97 --centroids vsearch.out
Reading file BioMarKs50k.fsa 100%
19073093 nt in 49958 seqs, min 32, max 497, avg 382
minseqlength 32: 42 sequences discarded.
Masking 100%
Sorting by length 100%
Counting k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 4301 Size min 1, max 932, avg 11.6
Singletons: 1856, 3.7% of seqs, 43.2% of clusters
[user@cn3144 46116226]$ 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 --threads $SLURM_CPUS_PER_TASK --usearch_global queries.fsa --db database.fsa --id 0.9 --alnout alnout.txt

Submit this job using the Slurm sbatch command, replacing # with appropriate values.

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

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

vsearch --threads $SLURM_CPUS_PER_TASK --usearch_global queries1.fsa --db database.fsa --id 0.9 --alnout alnout1.txt
vsearch --threads $SLURM_CPUS_PER_TASK --usearch_global queries2.fsa --db database.fsa --id 0.9 --alnout alnout2.txt
vsearch --threads $SLURM_CPUS_PER_TASK --usearch_global queries3.fsa --db database.fsa --id 0.9 --alnout alnout3.txt
vsearch --threads $SLURM_CPUS_PER_TASK --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