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USEARCH
Overview
USEARCH is a sequence analysis tool.
Versions 5.2.32 and 6.1.544, 8.0.1623 (pre-compiled 32 bit binaries) are installed on the CSF.
USEARCH is often used with QIIME. These pieces of software are installed separately on the CSF. If you wish to use them together you need to load USEARCH (see below) and QIIME.
Restrictions on use
This software is not open source. We have been granted a free academic license for the CSF by the developer. All users must observe the license terms on the usearch website, a copy of which is also available in the install directory. In particular it should be noted that:
- The software is not to be used for commercial purposes.
- You must not copy or make the software available to anyone else.
- You must cite your usage of the software as per the citation information on the usearch website.
If you are unsure whether your usage complies with the terms please contact its-ri-team@manchester.ac.uk.
To use the software you must agree to the terms, by emailing your confirmation you have read the above information to its-ri-team@manchester.ac.uk, and then you can be added to the usearch unix group which controls access.
Set up procedure
To access the software you must first load the modulefile for the version you are going to use:
module load apps/binapps/usearch/8.0.1623 OR module load apps/binapps/usearch/6.1.544 OR module load apps/binapps/usearch/5.2.32
Running the application
Please do not run USEARCH on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 6 # Use 6 cores in smp.pe. The number six will be passed to $NSLOTS # which is used to tell usearch how many threads to use. usearch -cluster_fast seqs.fasta -id 0.9 -threads $NSLOTS -centroids nr.fasta
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.