USEARCH is a sequence analysis tool.<\/p>\n
Versions 5.2.32 and 6.1.544, 8.0.1623 (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 (see below) and QIIME<\/a>.<\/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 If you are unsure whether your usage complies with the terms please contact its-ri-team@manchester.ac.uk<\/a>.<\/p>\n 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 To access the software you must first load the modulefile for the version you are going to use:<\/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 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.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2332","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2332","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=2332"}],"version-history":[{"count":19,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2332\/revisions"}],"predecessor-version":[{"id":4687,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2332\/revisions\/4687"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=2332"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
\n
usearch<\/code> unix group which controls access.<\/p>\nSet up procedure<\/h2>\n
\r\nmodule load apps\/binapps\/usearch\/8.0.1623\r\n\r\nOR\r\n\r\nmodule load apps\/binapps\/usearch\/6.1.544\r\n\r\nOR\r\n\r\nmodule load apps\/binapps\/usearch\/5.2.32\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\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
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n#$ -pe smp.pe 6 # Use 6 cores in smp.pe. The number six will be passed to $NSLOTS\r\n # which is used to tell usearch how many threads to use.\r\n\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