{"id":4340,"date":"2019-12-11T15:50:41","date_gmt":"2019-12-11T15:50:41","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4340"},"modified":"2019-12-11T15:50:41","modified_gmt":"2019-12-11T15:50:41","slug":"fastani","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/fastani\/","title":{"rendered":"FastANI"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/github.com\/ParBLiSS\/FastANI\">FastANI<\/a> is a program for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). It supports pairwise comparison of both complete and draft genome assemblies.<\/p>\n<p>Version 1.3 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 released under the <a href=\"https:\/\/github.com\/ParBLiSS\/FastANI\/blob\/master\/LICENSE\">Apache License 2.0<\/a> and all usage must adhere to that license.<\/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\/gcc\/fastani\/1.3\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run fastani 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 you require\r\nmodule load apps\/gcc\/fastani\/1.3\r\n\r\n# There are several ways in which FastANI can be run\r\n\r\n# One to one\r\nfastANI -q <em>QUERY_GENOME<\/em> -r <em>REFERENCE_GENOME<\/em> -o <em>OUTPUT_FILE<\/em>\r\n\r\n# One to Many\r\nfastANI -q <em>QUERY_GENOME<\/em> --rl <em>REFERENCE_LIST<\/em> -o <em>OUTPUT_FILE<\/em>\r\n\r\n# Many to Many\r\nfastANI --ql <em>QUERY_LIST<\/em> --rl <em>REFERENCE_LIST<\/em> -o <em>OUTPUT_FILE<\/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><em>Add<\/em> the following two lines to the above jobscript before the <code>fastANI<\/code> command to make the job a parallel (multi-core job):<\/p>\n<pre>\r\n#$ -pe smp.pe 8                    # Number of cores, can be 2--32.\r\nexport OMP_NUM_THREADS=$NSLOTS     # Inform FastANI how many cores it can use\r\n<\/pre>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/github.com\/ParBLiSS\/FastANI\">FastANI website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview FastANI is a program for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). It supports pairwise comparison of both complete and draft genome assemblies. Version 1.3 is installed on the CSF. Restrictions on use There are no restrictions on accessing this software on the CSF. It is released under the Apache License 2.0 and all usage must adhere to that license. Set up procedure We now recommend loading modulefiles within your jobscript so.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/fastani\/\">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-4340","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4340","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=4340"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4340\/revisions"}],"predecessor-version":[{"id":4341,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4340\/revisions\/4341"}],"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=4340"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}