{"id":6059,"date":"2012-02-22T11:15:46","date_gmt":"2012-02-22T09:15:46","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/?p=6059"},"modified":"2013-11-12T11:16:31","modified_gmt":"2013-11-12T09:16:31","slug":"velvet-3","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/velvet-3","title":{"rendered":"Velvet"},"content":{"rendered":"

Informazio orokorra<\/h2>\n

1.2.03 bertsioa. Velvet is a set of algorithms manipulating de Bruijn graphs for genomic and de novo transcriptomic Sequence assembly. It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute<\/a>. The tool takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.<\/p>\n

Begiratu ere instalatuta dagoen [intlink id=\u00bb6226″ type=\u00bbpost\u00bb]ABySS[\/intlink] eta biak konparatzen publikatu dugun artikulua<\/a>.<\/p>\n

Nola erabili<\/h2>\n

velveth<\/code> edo velvetg<\/code> exekutatzeko Torque ilara sisteman gehitu zuen scriptetan:<\/p>\n

\/software\/bin\/velvet\/velveth [velvet opzioak]<\/pre>\n
\/software\/bin\/velvet\/velvetg [velvet opzioak]<\/pre>\n
Erendimendua<\/h2>\n
Velvet OpenMP paralelizatzeko gaitasunarekin konpilatu da. Bere errendimendua neurtu dugu eta eskuragarri daude Velvet performance in the machines of the Computing Service of the UPV\/EHU<\/em><\/a> dokumentuan. Velvetek RAM memoria kopuru handia behar dukalkulu handietarako eta neurtu dugu ere. Formula simple batzuk lortu ditugu RAM memoria aurreikusteko sarrera fitxeroen arabera, horrela ikertzaileak bere ikerketa planifikatu dezake.<\/p>\n
Begiratu ere instalatuta dagoen [intlink id=\u00bb6226″ type=\u00bbpost\u00bb]ABySS[\/intlink] eta biak konparatzen publikatu dugun artikulua<\/a>.<\/p>\n
Informazio gehiago<\/h2>\n
Velvet web horrialdea<\/a>.
\nVelvet performance in the machines of the Computing Service of the UPV\/EHU<\/a>, errendimenduari buruzko txostena.
\nhpc blogean sarrera<\/a>: Velvet performance in the machines of the Computing Service of the UPV\/EHU<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"
Informazio orokorra 1.2.03 bertsioa. Velvet is a set of algorithms manipulating de Bruijn graphs for genomic and de novo transcriptomic Sequence assembly. It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute. The tool takes in short … Seguir leyendo Velvet<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_links_to":"","_links_to_target":""},"categories":[178,66],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6059"}],"collection":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/comments?post=6059"}],"version-history":[{"count":8,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6059\/revisions"}],"predecessor-version":[{"id":7101,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6059\/revisions\/7101"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=6059"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=6059"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=6059"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}