{"id":1610,"date":"2013-06-16T17:35:27","date_gmt":"2013-06-16T09:35:27","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1610"},"modified":"2013-06-16T18:11:00","modified_gmt":"2013-06-16T10:11:00","slug":"illumina%e6%95%b0%e6%8d%ae%e6%a8%a1%e6%8b%9f%e8%bd%af%e4%bb%b6","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1610","title":{"rendered":"Illumina\u6570\u636e\u6a21\u62df\u8f6f\u4ef6"},"content":{"rendered":"<p>\u73b0\u6709\u7684Illumina\u6570\u636e\u6a21\u62df\u8f6f\u4ef6\u6709\u4ee5\u4e0b\u51e0\u79cd\uff1a<\/p>\n<h1>1. pIRS<\/h1>\n<p>piRS: Profile-based Illumina pair-end reads simulator. \u662fBGI\u5f00\u53d1\u51fa\u6765\u7684\u8f6f\u4ef6\u3002\u4f7f\u7528C++\u548cPerl\u7f16\u5199\uff0c\u4e0b\u8f7d\u5730\u5740\uff1a<a href=\"ftp:\/\/ftp.genomics.org.cn\/pub\/pIRS\/\" target=\"_blank\">ftp:\/\/ftp.genomics.org.cn\/pub\/pIRS\/<\/a>\u3002pIRS\u540c\u65f6\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5f15\u5165variants\u7684\u5de5\u5177\uff0c\u4ece\u800c\u80fd\u6a21\u62df\u6742\u5408\u57fa\u56e0\u7ec4\u6570\u636e\u3002<\/p>\n<p>\u6587\u732e\uff1aXuesong Hu,Jianying Yuan,Yujian Shi,Jianliang Lu,Binghang Liu,Zhenyu Li,Yanxiang Chen,Desheng Mu,Hao Zhang,Nan Li,Zhen Yue,Fan Bai,Heng Li,and Wei Fan\u3002 pIRS: Profile-based Illumina pair-end reads simulator Bioinformatics (2012) 28 (11): 1533-1535<br \/>\n<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/28\/11\/1533.long\" target=\"_blank\">first published online April 15, 2012 doi:10.1093\/bioinformatics\/bts187 <\/a><\/p>\n<h1>2. ART<\/h1>\n<p>ART\u80fd\u6a21\u62dfIllumina, 454\u548cSOLiD\u7684\u8fd93\u4e2dNGS\u6570\u636e\uff0c\u5305\u62ec single-end, paired-end\u548cmate-pair\u4e09\u79cd\u7c7b\u578b\u7684\u6570\u636e\u3002ART\u662fNIH\u5f00\u53d1\u51fa\u7684\u8f6f\u4ef6\u3002\u5176\u5b98\u7f51\u7f51\u5740\u4e3a\uff1a<a href=\"http:\/\/www.niehs.nih.gov\/research\/resources\/software\/biostatistics\/art\/\" target=\"_blank\">http:\/\/www.niehs.nih.gov\/research\/resources\/software\/biostatistics\/art\/<\/a>\u3002\u73b0\u5728ART\u652f\u6301Illumina MiSeq\u7684\u6570\u636e\u6a21\u62df\u4e86\u3002\u8be5\u8f6f\u4ef6\u66f4\u65b0\u8f83\u591a\u8f83\u5feb\u3002<\/p>\n<p>Citation: <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/28\/4\/593.abstract\" target=\"_blank\">Weichun Huang, Leping Li, Jason R Myers, and Gabor T Marth. ART: a next-generation sequencing read simulator, Bioinformatics (2012) 28 (4): 593-594 <\/a><\/p>\n<h1>3. \u5176\u5b83\u8f6f\u4ef6<\/h1>\n<p>Wgsim from the Samtools package (<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/25\/16\/2078.full\" target=\"_blank\">Li et al., 2009<\/a>)<\/p>\n<p>MetaSim (<a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0003373\" target=\"_blank\">Richter et al., 2008<\/a>) for simulating metagenomic data<\/p>\n<p>Mason (<a href=\"http:\/\/seqan.de\/projects\/mason.html\" target=\"_blank\">http:\/\/seqan.de\/projects\/mason.html<\/a>) for both Illumina and 454 reads<\/p>\n<p>SimSeq (<a href=\"https:\/\/github.com\/jstjohn\/SimSeq\" target=\"_blank\">https:\/\/github.com\/jstjohn\/SimSeq<\/a>) for Illumina reads<\/p>\n<p>FlowSim (<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/26\/18\/i420.full\" target=\"_blank\">Balzer et al., 2010<\/a>) for 454 reads.<br \/>\n<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/29\/1\/119.full\" target=\"_blank\"><br \/>\nPBSIM: PacBio reads simulator&#8211;toward accurate genome assembly<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u73b0\u6709\u7684Illumina\u6570\u636e\u6a21\u62df\u8f6f\u4ef6\u6709\u4ee5\u4e0b\u51e0\u79cd\uff1a 1. pIRS piRS: Pr &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1610\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1610"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1610"}],"version-history":[{"count":6,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1610\/revisions"}],"predecessor-version":[{"id":1612,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1610\/revisions\/1612"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1610"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1610"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1610"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}