{"id":597,"date":"2013-05-02T09:47:07","date_gmt":"2013-05-02T09:47:07","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=597"},"modified":"2013-05-02T09:48:17","modified_gmt":"2013-05-02T09:48:17","slug":"velvet","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/velvet\/","title":{"rendered":"Velvet"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.<\/p>\n<p>Version 1.2.08 is available. The pre-compiled binaries which used the following options:<\/p>\n<pre>     \r\nCATEGORIES = 2\r\nMAXKMERLENGTH = 64\r\n<\/pre>\n<p>are installed.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>Velvet is open source under the GNU license. It is available to all users.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the executables please load the modulefile:<\/p>\n<pre>module load apps\/binapps\/velvet\/1.2.08<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run velvet on the login node. qrsh may be suitable for some work. Computationally intensive work should be submitted to the batch system.<\/p>\n<p>Velvet cannot be run on more than 1 core.<\/p>\n<h3>Examples<\/h3>\n<ul>\n<li>Create datasets needed by velvetg in the auto_351 folder via the one hour interactive queue:\n<pre>\r\nqrsh -l inter -l short -V -cwd velveth auto_351 31 -fastq unmapped351.fastq\r\n<\/pre>\n<\/li>\n<li>Output assembled contigs > 250bp as contigs.fa in the auto_351 folder via the one hour interactive queue:\n<pre>\r\nqrsh -l inter -l short -V -cwd velvetg auto_351 -min_contig_lgth 250\r\n<\/pre>\n<\/li>\n<li>To do both of the above via a batch job create a submission script containing the following:\n<pre>\r\n## SGE options\r\n## Inherit the login node environment\r\n#$ -V\r\n## Use the current directory\r\n#$ -cwd\r\n\r\nvelveth auto_351 31 -fastq unmapped351.fastq\r\nvelvetg auto_351 -min_contig_lgth 250\r\n<\/pre>\n<\/li>\n<\/ul>\n<h2>Further info<\/h2>\n<ul>\n<li>The <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/\">velvet website<\/a> and <a href=\"http:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/Manual.pdf\">manual<\/a>.<\/li>\n<li>Running the commands <code>velvetg<\/code> and <code>velveth<\/code> with no options give some help information.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. Version 1.2.08 is available. The pre-compiled binaries which used the following options: CATEGORIES = 2 MAXKMERLENGTH = 64 are installed. Restrictions on use Velvet is open source under the GNU license. It is available to all.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/velvet\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-597","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/597","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=597"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/597\/revisions"}],"predecessor-version":[{"id":601,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/597\/revisions\/601"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=597"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}