{"id":4071,"date":"2019-09-27T17:16:40","date_gmt":"2019-09-27T16:16:40","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4071"},"modified":"2021-07-27T17:42:06","modified_gmt":"2021-07-27T16:42:06","slug":"minimap2","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/minimap2\/","title":{"rendered":"Minimap2"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/github.com\/lh3\/minimap2\">Minimap2<\/a> is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.<\/p>\n<p>Version 2.17 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing this software on the CSF. It is release under the <a href=\"https:\/\/github.com\/lh3\/minimap2\/blob\/master\/LICENSE.txt\">MIT License<\/a> and all usage should adhere to that.<\/p>\n<h2>Set up procedure<\/h2>\n<p>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 <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>.<\/p>\n<p>Load one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/binapps\/minimap2\/2.17\r\nmodule load apps\/binapps\/minimap2\/2.21\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run minimap2 on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n# Load the version of the software you require\r\nmodule load apps\/binapps\/minimap2\/2.17\r\n\r\n# $NSLOTS is automatically set to 1 for a serial (1-core) job\r\nminimap2 -t $NSLOTS <em>args...<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 8     # Number of cores (can be 2--32)\r\n\r\n# Load the version of the software you require\r\nmodule load apps\/binapps\/minimap2\/2.17\r\n\r\n# $NSLOTS is automatically set to 1 for a serial (1-core) job\r\nminimap2 -t $NSLOTS <em>args...<\/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=\"https:\/\/github.com\/lh3\/minimap2\">minimap2 github website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Version 2.17 is installed on the CSF. Restrictions on use There are no restrictions on accessing this software on the CSF. It is release under the MIT License and all usage should adhere to that. Set up procedure We now recommend loading modulefiles within your jobscript so that you have a full record of how the.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/minimap2\/\">Read more &raquo;<\/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-4071","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4071","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=4071"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4071\/revisions"}],"predecessor-version":[{"id":5501,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4071\/revisions\/5501"}],"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=4071"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}