{"id":2554,"date":"2015-06-01T09:23:20","date_gmt":"2015-06-01T09:23:20","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=2554"},"modified":"2018-03-20T12:06:38","modified_gmt":"2018-03-20T12:06:38","slug":"spades","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/spades\/","title":{"rendered":"SPAdes"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>SPAdes &#8211; St. Petersburg genome assembler \u2013 is intended for both standard isolates and single-cell MDA bacteria assemblies.<\/p>\n<p>Versions 3.11.1, 3.10.1 and 3.5.0 are installed on the CSF.<\/p>\n<p>Note that other tools such as metaSPAdes are included in SPAdes. Run <code>spades.py -h<\/code> to see the command-line flags accepted by spades (for example <code>--meta<\/code>).<\/p>\n<h2>Restrictions on use<\/h2>\n<p>This software is open source and may be used by any CSF user. Please ensure that you cite your usage in any results or publications as per the <a href=\"http:\/\/spades.bioinf.spbau.ru\/release3.5.0\/manual.html#sec4\">developers documentation<\/a>.<\/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\/spades\/3.11.1\r\nmodule load apps\/binapps\/spades\/3.10.1\r\nmodule load apps\/binapps\/spades\/3.5.0\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run SPAdes on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission &#8211; coming soon<\/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#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n# $NSLOTS will be set automatically to 1 in a serial job\r\nspades.py --threads $NSLOTS -1 <em>file1.in<\/em> -2 <em>file2.in<\/em> -o <em>output_dir<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission &#8211; checking if possible<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores (2--24 permitted)\r\n\r\n# $NSLOTS will be set automatically to the number of cores given above\r\nspades.py --threads $NSLOTS -1 <em>file1.in<\/em> -2 <em>file2.in<\/em> -o <em>output_dir<\/em>\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=\"http:\/\/cab.spbu.ru\/files\/release3.11.1\/manual.html\">SPAdes version 3.11.1 website<\/a><\/li>\n<li><a href=\"http:\/\/cab.spbu.ru\/files\/release3.10.1\/manual.html\">SPAdes version 3.10.1 website<\/a><\/li>\n<li><a href=\"http:\/\/spades.bioinf.spbau.ru\/release3.5.0\/manual.html\">SPAdes version 3.5.0 website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview SPAdes &#8211; St. Petersburg genome assembler \u2013 is intended for both standard isolates and single-cell MDA bacteria assemblies. Versions 3.11.1, 3.10.1 and 3.5.0 are installed on the CSF. Note that other tools such as metaSPAdes are included in SPAdes. Run spades.py -h to see the command-line flags accepted by spades (for example &#8211;meta). Restrictions on use This software is open source and may be used by any CSF user. Please ensure that you cite.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/spades\/\">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-2554","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2554","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=2554"}],"version-history":[{"count":8,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2554\/revisions"}],"predecessor-version":[{"id":4620,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2554\/revisions\/4620"}],"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=2554"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}