{"id":6121,"date":"2012-03-09T01:30:44","date_gmt":"2012-03-08T23:30:44","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/?p=6121"},"modified":"2012-03-09T01:32:16","modified_gmt":"2012-03-08T23:32:16","slug":"clean_reads-2","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/clean_reads-2","title":{"rendered":"Clean_reads"},"content":{"rendered":"<h2>Informazio orokorra<\/h2>\n<p>0.2.2 bertsioa. <code>clean_reads<\/code> programak Sanger, 454, Illumina eta Solid NGS (next generation sequencing) datuak garbitzen ditu. Kendu ditzake<\/p>\n<ul>\n<li>Kalitate txarreko aldeak<\/li>\n<li>Adaptadoreak<\/li>\n<li>Vektoreak<\/li>\n<li>Espresio regularrak<\/li>\n<\/ul>\n<p>Kalitate eratainan eta luzeeran oinarritutako kalitate txarreko irakurketak eliminatu ditzazke ere. Paraleloan exekutatu daiteke.<\/p>\n<h2>Nola erabili<\/h2>\n<p>Kola sistemara lanak bidaltzeko\u00a0 erabili dezakezue<\/p>\n<pre>send_clean_reads<\/pre>\n<p>komandoa zinek galdera batzuen bitartez skripta prestatu eta bidaliko du.<\/p>\n<h2>Errendimendua<\/h2>\n<p><code>clean_reads<\/code> programak paraleloan exekutatu daiteke eta ondo eskalatzen du 8 kore arte. 12 koreentzako errendimendua asko jaisten da. Taulan ikus daite benchmarken emaitzak. Xeon E5645 procesadoreak erabiliz 12 koretako nodoan.<\/p>\n<table border=\"0\" align=\"center\">\n<caption>Exekuzio denbora segundutan kore kopuruaren arabera<\/caption>\n<tbody>\n<tr>\n<td><strong>koreak<\/strong><\/td>\n<td>1<\/td>\n<td>4<\/td>\n<td>8<\/td>\n<td>12<\/td>\n<\/tr>\n<tr>\n<td>Denbora (s)<\/td>\n<td>1600<\/td>\n<td>422<\/td>\n<td>246<\/td>\n<td>238<\/td>\n<\/tr>\n<tr>\n<td>Azelerazioa<\/td>\n<td>1<\/td>\n<td>3.8<\/td>\n<td>6.5<\/td>\n<td>6.7<\/td>\n<\/tr>\n<tr>\n<td>Errendimendua (%)<\/td>\n<td>100<\/td>\n<td>95<\/td>\n<td>81<\/td>\n<td>56<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>Ondorengo komandoa exekutatu da<\/p>\n<pre>clean_reads -i in.fastq -o out.fastq -p illumina -f fastq -g fastq -a a.fna -d UniVec -n 20 --qual_threshold=20 --only_3_end False -m 60 -t 12<\/pre>\n<h2>Informazio gehiago<\/h2>\n<p><a title=\"clean_reads home\" href=\"http:\/\/bioinf.comav.upv.es\/clean_reads\/index.html\" target=\"_blank\">clean_reads web orrialdea<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Informazio orokorra 0.2.2 bertsioa. clean_reads programak Sanger, 454, Illumina eta Solid NGS (next generation sequencing) datuak garbitzen ditu. Kendu ditzake Kalitate txarreko aldeak Adaptadoreak Vektoreak Espresio regularrak Kalitate eratainan eta luzeeran oinarritutako kalitate txarreko irakurketak eliminatu ditzazke ere. Paraleloan exekutatu daiteke. Nola erabili Kola sistemara lanak bidaltzeko\u00a0 erabili dezakezue send_clean_reads komandoa zinek galdera batzuen bitartez &hellip; <a href=\"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/clean_reads-2\" class=\"more-link\">Seguir leyendo <span class=\"screen-reader-text\">Clean_reads<\/span> <span class=\"meta-nav\">&rarr;<\/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\/6121"}],"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=6121"}],"version-history":[{"count":3,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6121\/revisions"}],"predecessor-version":[{"id":6125,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6121\/revisions\/6125"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=6121"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=6121"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=6121"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}