{"id":843,"date":"2018-03-06T16:46:06","date_gmt":"2018-03-06T16:46:06","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=843"},"modified":"2018-03-07T09:06:04","modified_gmt":"2018-03-07T09:06:04","slug":"jellyfish","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/jellyfish\/","title":{"rendered":"JellyFish"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/www.genome.umd.edu\/jellyfish.html\">Jellyfish<\/a> Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the &#8220;compare-and-swap&#8221; CPU instruction to increase parallelism.<\/p>\n<p>Version 2.2.7 is installed on the iCSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>The software is free to use, Jellyfish is distributed as source code under the GPL license Please see the <a href=\"http:\/\/www.gnu.org\/licenses\/gpl-3.0-standalone.html\">GPL License page<\/a> for more details.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>module load apps\/gcc\/jellyfish\/2.2.7\r\n<\/pre>\n<h2>Running the application<\/h2>\n<pre>jellyfish &lt;cmd&gt; [options] arg...\r\nWhere &lt;cmd&gt; is one of: count, bc, info, stats, histo, dump, merge, query, cite, mem, jf.\r\nOptions:\r\n  --version        Display version\r\n  --help           Display this message\r\n\r\n<\/pre>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/www.genome.umd.edu\/jellyfish.html\">Jellyfish website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the &#8220;compare-and-swap&#8221; CPU instruction to increase parallelism. Version 2.2.7 is installed on the iCSF. Restrictions on use The.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/jellyfish\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-843","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/843","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=843"}],"version-history":[{"count":7,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/843\/revisions"}],"predecessor-version":[{"id":853,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/843\/revisions\/853"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=843"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}