{"id":8067,"date":"2015-09-11T13:31:42","date_gmt":"2015-09-11T11:31:42","guid":{"rendered":"http:\/\/www.ehu.eus\/sgi\/?p=8067"},"modified":"2015-09-28T14:11:56","modified_gmt":"2015-09-28T12:11:56","slug":"idba-ud-3","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/idba-ud-3","title":{"rendered":"IDBA-UD"},"content":{"rendered":"<h2>Informazio orokorra<\/h2>\n<p>IDBA-UD 1.1.1 is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.<\/p>\n<h2>Nola erabili<\/h2>\n<p>Lanak koletara bidaltzeko ondorengo komandoa erabili daiteke<\/p>\n<pre>send_idba-ud<\/pre>\n<p>eta galdera batzuk erantzun eta gero bidaliko du lana.<\/p>\n<h2>Erendimendua<\/h2>\n<p>IDBA-UD ondo eskalatzen du 8 koreetaraino. Hortik gora ez dugu inongo hobenkuntzarik nabaritu. Benchmark <code>--mimk 40 --step 20<\/code> aukerekin egin da eta step murriztu dugunean okerrago paralelizatzen du. Bigarren taulan ere step 10-ekin errendimendua ez da ona 4 koretik gora.<\/p>\n<table>\n<tbody>\n<tr>\n<td><\/td>\n<td><\/td>\n<td colspan=\"2\" align=\"center\" valign=\"middle\">kore 1 oinarri bezala<\/td>\n<td colspan=\"2\" align=\"center\" valign=\"middle\">2 kore oinarri bezala<\/td>\n<\/tr>\n<tr>\n<td>Koreak<\/td>\n<td>Denbora (s)<\/td>\n<td>Azelerazioa<\/td>\n<td>Errendimendua (%)<\/td>\n<td>Azelerazioa<\/td>\n<td>Errendimendua<\/td>\n<\/tr>\n<tr>\n<td>1<\/td>\n<td>480<\/td>\n<td>1<\/td>\n<td>100<\/td>\n<td><\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>2<\/td>\n<td>296<\/td>\n<td>1.6<\/td>\n<td>81<\/td>\n<td>1.0<\/td>\n<td>100<\/td>\n<\/tr>\n<tr>\n<td>4<\/td>\n<td>188<\/td>\n<td>2.6<\/td>\n<td>64<\/td>\n<td>1.6<\/td>\n<td>79<\/td>\n<\/tr>\n<tr>\n<td>8<\/td>\n<td>84<\/td>\n<td>5.7<\/td>\n<td>71<\/td>\n<td>3.5<\/td>\n<td>88<\/td>\n<\/tr>\n<tr>\n<td>12<\/td>\n<td>92<\/td>\n<td>5.2<\/td>\n<td>43<\/td>\n<td>3.2<\/td>\n<td>54<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>Bigarren benchmarka fitxategin handiago batekin egin dugu, 10 milio basetakoa eta <code>--mink 20 --step 10 --min_support 2<\/code> aukerekin. Ikusten dugu konportamendu erregularragoa eta nola 4 koreetatik gora ez duen ondo eskalatzen.<\/p>\n<table>\n<tbody>\n<tr>\n<td>Koreak<\/td>\n<td>Denbora (s)<\/td>\n<td>Azelerazioa<\/td>\n<td>errendimendua (%)<\/td>\n<\/tr>\n<tr>\n<td>1<\/td>\n<td>13050<\/td>\n<td>1<\/td>\n<td>100<\/td>\n<\/tr>\n<tr>\n<td>2<\/td>\n<td>6675<\/td>\n<td>2.0<\/td>\n<td>98<\/td>\n<\/tr>\n<tr>\n<td>4<\/td>\n<td>3849<\/td>\n<td>3.4<\/td>\n<td>85<\/td>\n<\/tr>\n<tr>\n<td>8<\/td>\n<td>3113<\/td>\n<td>4.2<\/td>\n<td>52<\/td>\n<\/tr>\n<tr>\n<td>16<\/td>\n<td>2337<\/td>\n<td>5.6<\/td>\n<td>35<\/td>\n<\/tr>\n<tr>\n<td>20<\/td>\n<td>2409<\/td>\n<td>5.4<\/td>\n<td>27<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h2>Informazio gehigo<\/h2>\n<p><a href=\"http:\/\/i.cs.hku.hk\/~alse\/hkubrg\/projects\/idba_ud\/index.html\" target=\"_blank\">IDBA-UD<\/a> web orrialdea.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Informazio orokorra IDBA-UD 1.1.1 is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low &hellip; <a href=\"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/idba-ud-3\" class=\"more-link\">Seguir leyendo <span class=\"screen-reader-text\">IDBA-UD<\/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\/8067"}],"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=8067"}],"version-history":[{"count":4,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/8067\/revisions"}],"predecessor-version":[{"id":8151,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/8067\/revisions\/8151"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=8067"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=8067"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=8067"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}