{"id":6131,"date":"2012-03-09T01:35:30","date_gmt":"2012-03-08T23:35:30","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/?p=6131"},"modified":"2012-03-09T01:46:45","modified_gmt":"2012-03-08T23:46:45","slug":"clean-reads","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/scientific-software\/clean-reads","title":{"rendered":"Clean reads"},"content":{"rendered":"<h2>General information<\/h2>\n<p>0.2.2 Version. <code>clean_reads<\/code> cleans NGS (Sanger, 454, Illumina and solid) reads. It can trim:<\/p>\n<ul>\n<li>bad quality regions<\/li>\n<li>adaptors<\/li>\n<li>vectors<\/li>\n<li>regular expresssions<\/li>\n<\/ul>\n<p>It also filters out the reads that do not meet a minimum quality criteria based on the sequence length and the mean quality. It can run in parallel.<\/p>\n<h2>Ho to use<\/h2>\n<p>To submit <code>clean_reads<\/code> jobs to the queue system execute the command<\/p>\n<pre>send_clean_reads<\/pre>\n<p>It will ask few questions to build the script and submit it to the queue.<\/p>\n<h2>Performance<\/h2>\n<p><code>clean_reads<\/code> can be executed in parallel and scales well up to 8 cores. For 12 cores the performance is very poor. In the table 1 we show the results of the benchmark. They have been executed in a 12 cores node with E5645 Xeon processors.<\/p>\n<table border=\"0\" align=\"center\">\n<caption>Execution time in seconds as a function of the number of cores<\/caption>\n<tbody>\n<tr>\n<td><strong>cores<\/strong><\/td>\n<td>1<\/td>\n<td>4<\/td>\n<td>8<\/td>\n<td>12<\/td>\n<\/tr>\n<tr>\n<td>Time (s)<\/td>\n<td>1600<\/td>\n<td>422<\/td>\n<td>246<\/td>\n<td>238<\/td>\n<\/tr>\n<tr>\n<td>Speedup<\/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>Performance (%)<\/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>The used command has been<\/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>More information<\/h2>\n<p><a title=\"clean_reads home\" href=\"http:\/\/bioinf.comav.upv.es\/clean_reads\/index.html\" target=\"_blank\">clean_reads web page<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>General information 0.2.2 Version. clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads. It can trim: bad quality regions adaptors vectors regular expresssions It also filters out the reads that do not meet a minimum quality criteria based on the sequence length and the mean quality. It can run in parallel. Ho to use To &hellip; <a href=\"https:\/\/www.ehu.eus\/sgi\/scientific-software\/clean-reads\" 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":[239,196],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6131"}],"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=6131"}],"version-history":[{"count":3,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6131\/revisions"}],"predecessor-version":[{"id":6135,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6131\/revisions\/6135"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=6131"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=6131"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=6131"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}