USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

• http://www.drive5.com/usearch/

• Module Name: usearch (see the modules page for more information)
• Single-threaded
• Environment variables set:
  • usearch -- path to usearch
  • USEARCH_EXAMPLES -- examples

Allocate an interactive session and run the program. Sample session:

[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 usearch
[user@cn3144 ~]$ cp -R $USEARCH_EXAMPLES/hmptut .
[user@cn3144 ~]$ cd hmptut/scripts
[user@cn3144 ~]$ bash run.bash

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

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

#!/bin/bash
# --- This file is usearch.sh --
  
module load usearch
usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta

Submit this job using the Slurm sbatch command.

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

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

usearch -cluster_fast seqs.fasta.1 -id 0.9 -centroids nr.fasta
usearch -cluster_fast seqs.fasta.2 -id 0.9 -centroids nr.fasta
usearch -cluster_fast seqs.fasta.3 -id 0.9 -centroids nr.fasta
usearch -cluster_fast seqs.fasta.4 -id 0.9 -centroids nr.fasta

Submit this job using the swarm command.

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