{"id":2581,"date":"2015-06-12T10:02:12","date_gmt":"2015-06-12T10:02:12","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=2581"},"modified":"2015-06-12T10:04:58","modified_gmt":"2015-06-12T10:04:58","slug":"vsearch","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/vsearch\/","title":{"rendered":"vsearch"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>vsearch is a sequence analysis tool.<\/p>\n<p>Version 1.1.3 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>This software may be used by all users, it is open-source.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>\r\nmodule load apps\/binapps\/vsearch\/1.1.3\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run vsearch on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\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\nvsearch113 -cluster_fast combined.fasta -id 0.97 -uc results.uc -centroids centroids.fasta\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\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 $NSLOTS\r\n                    #  which is used to tell usearch how many threads to use.\r\n\r\nvsearch113 -cluster_fast combined.fasta -id 0.97 --threads=$NSLOTS -uc results.uc -centroids centroids.fasta\r\n\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/github.com\/torognes\/vsearch\/wiki\">vsearch github site<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview vsearch is a sequence analysis tool. Version 1.1.3 is installed on the CSF. Restrictions on use This software may be used by all users, it is open-source. Set up procedure To access the software you must first load the modulefile: module load apps\/binapps\/vsearch\/1.1.3 Running the application Please do not run vsearch on the login node. Jobs should be submitted to the compute nodes via batch. Serial batch job submission Make sure you have the.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/vsearch\/\">Read more &raquo;<\/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-2581","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2581","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=2581"}],"version-history":[{"count":4,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2581\/revisions"}],"predecessor-version":[{"id":2585,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2581\/revisions\/2585"}],"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=2581"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}