{"id":8051,"date":"2015-09-11T10:31:04","date_gmt":"2015-09-11T08:31:04","guid":{"rendered":"http:\/\/www.ehu.eus\/sgi\/?p=8051"},"modified":"2015-09-28T14:11:59","modified_gmt":"2015-09-28T12:11:59","slug":"idba-ud","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/software-de-calculo\/idba-ud","title":{"rendered":"IDBA-UD"},"content":{"rendered":"

Informaci\u00f3n general<\/h2>\n

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

C\u00f3mo usar<\/h2>\n

Para enviar trabajos a la cola se puede usar el comando<\/p>\n

send_idba-ud<\/pre>\n
que realiza unas preguntas para configurar el c\u00e1lculo.<\/p>\n
Rendimiento<\/h2>\n
IDBA-UD se ejecuta en paralelo con un buen rendimiento medido hasta por lo menos 8 cores. Por encima no se han medido mejoras apreciables. El benchmark se ha realizado con --mimk 40 --step 20<\/code>.\u00a0 Por alg\u00fan motivo este c\u00e1lculo tiene un salto cualitativo apreciable de 1 a dos cores. Si se pone un step de 10 el rendimiento a varios cores empeora como se observa en la segunda tabla.<\/p>\n\n\n\n\n\n\n\n\n\n
<\/td>\n<\/td>\n1 core como base<\/td>\n2 cores como base<\/td>\n<\/tr>\n
Cores<\/td>\nTiempo (s)<\/td>\nAceleraci\u00f3n<\/td>\nRendimiento (%)<\/td>\nAceleraci\u00f3n<\/td>\nRendimiento (%)<\/td>\n<\/tr>\n
1<\/td>\n\u00a0480<\/td>\n1<\/td>\n100<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
2<\/td>\n296<\/td>\n\u00a01.6<\/td>\n\u00a081<\/td>\n1.0<\/td>\n100<\/td>\n<\/tr>\n
4<\/td>\n188<\/td>\n2.6<\/td>\n64<\/td>\n1.6<\/td>\n79<\/td>\n<\/tr>\n
8<\/td>\n\u00a084<\/td>\n5.7<\/td>\n71<\/td>\n3.5<\/td>\n88<\/td>\n<\/tr>\n
12<\/td>\n92<\/td>\n5.2<\/td>\n43<\/td>\n3.2<\/td>\n54<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
El segundo benchmark se ha realizado con un fichero mayor, con 10 millones de bases y las opciones --mink 20 --step 10 --min_support 2<\/code>. Observamos un comportamiento m\u00e1s regular que en el benchmark anterior y como la paralelizaci\u00f3n es buena hasta los 4 cores.<\/p>\n\n\n\n\n\n\n\n\n\n
Cores<\/td>\nTiempo (s)<\/td>\nAceleraci\u00f3n<\/td>\nRendimiento (%)<\/td>\n<\/tr>\n
1<\/td>\n13050<\/td>\n1<\/td>\n100<\/td>\n<\/tr>\n
2<\/td>\n6675<\/td>\n2.0<\/td>\n98<\/td>\n<\/tr>\n
4<\/td>\n3849<\/td>\n3.4<\/td>\n85<\/td>\n<\/tr>\n
8<\/td>\n3113<\/td>\n4.2<\/td>\n52<\/td>\n<\/tr>\n
16<\/td>\n2337<\/td>\n5.6<\/td>\n35<\/td>\n<\/tr>\n
20<\/td>\n2409<\/td>\n5.4<\/td>\n27<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
M\u00e1s informaci\u00f3n<\/h2>\n
P\u00e1gina web de IDBA-UD<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"
Informaci\u00f3n general 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 … Seguir leyendo IDBA-UD<\/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":[176,3],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/8051"}],"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=8051"}],"version-history":[{"count":5,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/8051\/revisions"}],"predecessor-version":[{"id":8141,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/8051\/revisions\/8141"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=8051"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=8051"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=8051"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}