USEARCH is a sequence analysis tool.<\/p>\n
Versions 8.0.1623 and 11.0.667 (pre-compiled 32 bit binaries) are installed on the CSF.<\/p>\n
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 and QIIME modulefiles (see below).<\/p>\n
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>, a copy of which is also available in the install directory. In particular it should be noted that:<\/p>\n To use the software you must agree to the terms, please complete our help form<\/a> confirming your agreement and then you can be added to the We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n To access the software you must first load one<\/em> of the following modulefiles:<\/p>\n If you wish to run QIIME please also load the following modulefiles:<\/p>\n Please do not run USEARCH on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using:<\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using:<\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview USEARCH is a sequence analysis tool. Versions 8.0.1623 and 11.0.667 (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 and QIIME modulefiles (see below). Restrictions on use This software is not open source. We have been granted a free academic license for the CSF by the.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2212","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2212","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=2212"}],"version-history":[{"count":11,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2212\/revisions"}],"predecessor-version":[{"id":9903,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2212\/revisions\/9903"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=2212"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\n
usearch<\/code> unix group which controls access.<\/p>\nSet up procedure<\/h2>\n
module load apps\/binapps\/usearch\/11.0.667\r\nmodule load apps\/binapps\/usearch\/8.0.1623\r\n<\/pre>\n
module load apps\/bioinf\r\nmodule load apps\/qiime\/1.9.1 # Use module search apps\/qiime to check for newer versions<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n\r\n### We now load the modulefile in the jobscript, for example:\r\nmodule load apps\/binapps\/usearch\/11.0.667\r\n\r\nusearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Parallel batch job submission<\/h3>\n
#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n#$ -pe smp.pe 6 # Use 6 cores in smp.pe (2--32 permitted)\r\n\r\n### We now load the modulefile in the jobscript, for example:\r\nmodule load apps\/binapps\/usearch\/11.0.667\r\n\r\n### $NSLOTS is automatically set to number of cores requested above\r\nusearch -cluster_fast seqs.fasta -id 0.9 -threads $NSLOTS -centroids nr.fasta\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
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Updates<\/h2>\n