{"id":1075,"date":"2011-07-26T16:51:43","date_gmt":"2011-07-26T14:51:43","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2011\/07\/26\/velvet-and-bioperl"},"modified":"2022-09-26T20:00:58","modified_gmt":"2022-09-26T18:00:58","slug":"velvet-and-bioperl","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/26\/velvet-and-bioperl\/","title":{"rendered":"Velvet and BioPerl"},"content":{"rendered":"We recently ported <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/\">Velvet<\/a>, a short <a href=\"http:\/\/en.wikipedia.org\/wiki\/Sequence_assembly\">sequence assembler<\/a>, to our cluster.\u00a0 It can be compiled with multi-threading via OMP, however there does not seem to be an elegant way to control its behaviour in a clustered environment other than to use PBS directives to book an entire node.\u00a0 The problem here is that a user would need a completely free node to start with.\u00a0 We'll see how well this works, however we may elect to recompile the application without OMP support.\r\n\r\nIn addition to Velvet we installed the <a href=\"http:\/\/bioinformatics.net.au\/software.velvetoptimiser.shtml\">Velvet Optimiser<\/a>.\u00a0 This is very simple to install, however one of the requirements is apparently <a href=\"http:\/\/www.bioperl.org\/wiki\/Getting_BioPerl\">BioPerl<\/a>.\u00a0 This install was a bit more complex and required an install base directive to ensure that the scripts ended up in the NFS application mount.\r\n\r\nVelvet is memory hungry, on a node with 4GB of RAM an assembly took over an hour to reconstruct, whereas on a node with 24GB or RAM the same read took just over a minute.\u00a0 We're hoping that this application is swiftly ported to Grid format as our site has a distinct lack of large memory machines.\r\n\r\n<img src=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/assemble.png\" alt=\"Assemble\" border=\"0\" \/>","protected":false},"excerpt":{"rendered":"<p>We recently ported <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/\">Velvet<\/a>, a short <a href=\"http:\/\/en.wikipedia.org\/wiki\/Sequence_assembly\">sequence assembler<\/a>, to our cluster.&nbsp; It can be compiled with multi-threading via OMP, however there does not seem to be an elegant way to control its behaviour in a clustered environment other than to use PBS directives to book an entire node.&nbsp; The problem here is that a user would need a completely free node to start with.&nbsp; We&#8217;ll see how well this works, however we may elect to recompile the application without OMP support.<\/p>\n<p>In addition to Velvet we installed the <a href=\"http:\/\/bioinformatics.net.au\/software.velvetoptimiser.shtml\">Velvet Optimiser<\/a>.&nbsp; This is very simple to install, however one of the requirements is apparently <a href=\"http:\/\/www.bioperl.org\/wiki\/Getting_BioPerl\">BioPerl<\/a>.&nbsp; This install was a bit more complex and required an install base directive to ensure that the scripts ended up in the NFS application mount.<\/p>\n<p>Velvet is memory hungry, on a node with 4GB of RAM an assembly took over an hour to reconstruct, whereas on a node with 24GB or RAM the same read took just over a minute.&nbsp; We&#8217;re hoping that this application is swiftly ported to Grid format as our site has a distinct lack of large memory machines.<\/p>\n<p><img decoding=\"async\" src=\"http:\/\/blogs.uct.ac.za\/gallery\/1253\/assemble.png\" border=\"0\" alt=\"Assemble\"><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[9,4],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - 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