{"id":1087,"date":"2011-07-09T22:25:28","date_gmt":"2011-07-09T20:25:28","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2011\/07\/09\/sequencing-suite"},"modified":"2015-08-14T14:04:25","modified_gmt":"2015-08-14T12:04:25","slug":"sequencing-suite","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/","title":{"rendered":"Sequencing suite"},"content":{"rendered":"We spent this week porting a suite of packages for short sequence analysis: <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/\">Velvet<\/a>, <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/oases\/\">Oases<\/a>, <a href=\"http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/download.html\">FastX<\/a>, <a href=\"http:\/\/www.bioinformatics.bbsrc.ac.uk\/projects\/download.html#fastqc\">FastQC<\/a> and <a href=\"http:\/\/maq.sourceforge.net\/maq-man.shtml\">Maq<\/a>.\r\n\r\nWe've only tested Velvet so far, it's memory hungry and seems to run best on the 400 series blades by several orders of magnitude. It's also OMP capable, but not MPI, which means instances need to be launched carefully in order to avoid hogging CPU resources.\r\n\r\n&nbsp;","protected":false},"excerpt":{"rendered":"<p>We spent this week porting a suite of packages for short sequence analysis: <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/\">Velvet<\/a>, <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/oases\/\">Oases<\/a>, <a href=\"http:\/\/hannonlab.cshl.edu\/fastx_toolkit\/download.html\">FastX<\/a>, <a href=\"http:\/\/www.bioinformatics.bbsrc.ac.uk\/projects\/download.html#fastqc\">FastQC<\/a> and <a href=\"http:\/\/maq.sourceforge.net\/maq-man.shtml\">Maq<\/a>.<\/p>\n<p>We&#8217;ve only tested Velvet so far, it&#8217;s memory hungry and seems to run best on the 400 series blades by several orders of magnitude. It&#8217;s also OMP capable, but not MPI, which means instances need to be launched carefully in order to avoid hogging CPU resources.<\/p>\n<p>&nbsp;<\/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 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Sequencing suite - UCT HPC<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Sequencing suite - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"We spent this week porting a suite of packages for short sequence analysis: Velvet, Oases, FastX, FastQC and Maq.We&#039;ve only tested Velvet so far, it&#039;s memory hungry and seems to run best on the 400 series blades by several orders of magnitude. It&#039;s also OMP capable, but not MPI, which means instances need to be launched carefully in order to avoid hogging CPU resources.&nbsp;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2011-07-09T20:25:28+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2015-08-14T12:04:25+00:00\" \/>\n<meta name=\"author\" content=\"Andrew Lewis\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Andrew Lewis\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/\"},\"author\":{\"name\":\"Andrew Lewis\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/c183ad1c0a1063124a72d63963ae9c7e\"},\"headline\":\"Sequencing suite\",\"datePublished\":\"2011-07-09T20:25:28+00:00\",\"dateModified\":\"2015-08-14T12:04:25+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/\"},\"wordCount\":67,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"application\",\"hpc\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/07\/09\/sequencing-suite\/\",\"name\":\"Sequencing suite - 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