{"id":1733,"date":"2013-07-05T16:08:36","date_gmt":"2013-07-05T08:08:36","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1733"},"modified":"2013-07-05T20:27:15","modified_gmt":"2013-07-05T12:27:15","slug":"%e5%9f%ba%e5%9b%a0%e7%bb%84%e8%8d%89%e5%9b%be%e7%9a%84gap-closer%e8%bd%af%e4%bb%b6%ef%bc%9agapfiller","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1733","title":{"rendered":"\u57fa\u56e0\u7ec4\u8349\u56fe\u7684gap closer\u8f6f\u4ef6\uff1aGapFiller"},"content":{"rendered":"<h1>1. GapFiller\u7b80\u4ecb<\/h1>\n<p>\u7ec4\u88c5\u51fa\u6765\u7684\u57fa\u56e0\u7ec4\u8349\u56fe\u7684scaffold\u9700\u8981\u8fdb\u4e00\u6b65\u8fdb\u884cgaps\u7684\u5173\u95ed\u3002\u8fdb\u884c\u8fd9\u6837\u529f\u80fd\u7684\u8f6f\u4ef6\u6709\uff1a<a href=\"http:\/\/soap.genomics.org.cn\/soapdenovo.html\" target=\"_blank\">SOAPdenovo GapCloser v1.12r6<\/a>; <a href=\"http:\/\/sourceforge.net\/projects\/image2\/\" target=\"_blank\">IMAGE<\/a>; <a href=\"http:\/\/www.baseclear.com\/landingpages\/basetools-a-wide-range-of-bioinformatics-solutions\/gapfiller\/\" target=\"_blank\">GapFiller<\/a>.<\/p>\n<p>GapFiller\u6587\u7ae0\u53d1\u8868\u5728Genome Biology\u4e0a\uff1a<a href=\"http:\/\/genomebiology.com\/content\/13\/6\/R56#B6\" target=\"_blank\">Boetzer M,Pirovano W. 2012. Toward almost closed genomes with GapFiller. Genome Biol.13:R56<\/a>\u3002\u4ece\u6587\u7ae0\u53ef\u4ee5\u5b8c\u5168\u660e\u767d\u8be5\u8f6f\u4ef6closing gap\u7684\u539f\u7406\u3002<\/p>\n<p>GapFiller\u9700\u8981\u8f93\u5165scaffold\u5e8f\u5217(FASTA)\u548cNGS paired-read\u6570\u636e(FASTA or FASTAQ)\uff0c\u8f93\u51faFASTA\u683c\u5f0f\u6587\u4ef6\u3002\u8be5\u8f6f\u4ef6\u7684\u83b7\u5f97\u9700\u8981\u586b\u5199\u4e00\u4e9b\u90ae\u7bb1\u548c\u5355\u4f4d\u4fe1\u606f\u3002\u5546\u4e1alicense\u9700\u8981\u82b1\u94b1\uff1b\u5b66\u672f\u6027\u9700\u8981\u5f15\u7528\u5176\u6587\u7ae0\u3002<\/p>\n<h1>2. GapFiller\u5b89\u88c5<\/h1>\n<p>\u4e0b\u8f7dGapFiller\u7684\u5b89\u88c5\u5305\uff0c\u89e3\u538b\u7f29\u540e\uff0c\u91cc\u9762\u5305\u542bbowtie\u3001bwa\u548cexample\u51713\u4e2a\u6587\u4ef6\uff0c\u5176\u6700\u91cd\u8981\u7684\u662fGapFiller.pl\u6587\u4ef6\uff0c\u4e3a\u4e3b\u7a0b\u5e8f\u3002\u8fd8\u67092\u4e2aPDF\u683c\u5f0f\u7684manual\u6587\u4ef6\u3002<\/p>\n<h1>3. GapFiller\u7684\u4f7f\u7528<\/h1>\n<p>\u76f4\u63a5\u8fd0\u884c\u4e3b\u7a0b\u5e8f\uff0c\u4f1a\u7ed9\u51fa\u8f6f\u4ef6\u7684\u53c2\u6570\u8bf4\u660e\uff0c\u5982\u4e0b\uff1a<\/p>\n<p><code>-l library\u6587\u4ef6<br \/>\n-s scaffold\u5e8f\u5217\u7684fasta\u6587\u4ef6<br \/>\n-m default:29 \u548cgap\u8fb9\u7f18\u91cd\u53e0\u7684\u6700\u5c0f\u78b1\u57fa\u6570,\u8be5\u6570\u503c\u6700\u597d\u8bbe\u7f6e\u6bd4reads\u7684\u957f\u5ea6\u5c0f\u4e00\u70b9\u70b9\u7684\u6570\u3002\u6bd4\u598236bp\u957f\u5ea6\u7684reads\uff0c\u8bbe\u7f6e\u8be5\u503c\u4e3a30~35.<br \/>\n-o default:2 \u5728\u8865\u6d1e\u65f6\uff0c\u5ef6\u4f38\u4e00\u4e2a\u78b1\u57fa\u6700\u5c0f\u9700\u8981\u7684reads\u6570.<br \/>\n-r default:0.7 \u5728\u8865\u6d1e\u65f6\uff0c\u81f3\u5c11\u6709\u8be5\u6bd4\u4f8breads\u7684\u78b1\u57fa\u4e00\u81f4\uff0c\u624d\u80fd\u5bf9\u8be5\u78b1\u57fa\u4f4d\u70b9\u8fdb\u884c\u5ef6\u4f38\u3002<br \/>\n-d default:50 gap\u90e8\u5206\u5e8f\u5217\u7684\u5141\u8bb8\u7684\u6700\u5927\u5dee\u5f02\u3002\u586b\u8865gap\u540e\uff0c\u82e5\u503c\u201c\u586b\u8865\u4e0a\u7684\u5e8f\u5217\u957f\u5ea6 - gap\u957f\u5ea6\u201d\u5927\u4e8e\u8be5\u9608\u503c\uff0c\u5219\u505c\u6b62\u8865\u6d1e\uff1b\u82e5\u5c0f\u4e8e\u8be5\u9608\u503c\uff0c\u5219\u4e0d\u8fdb\u884c\u878d\u5408\u3002<br \/>\n-n default:10 \u5728\u4e00\u4e2ascaffold\u4e2d\u5bf9\u90bb\u8fd1\u7684\u4e24\u4e2acontigs\u8fdb\u884c\u878d\u5408\u6240\u9700\u8981\u6700\u5c0f\u91cd\u53e0\u7684\u78b1\u57fa\u6570\u3002<br \/>\n-t default:10 \u7531\u4e8egap\u8fb9\u7f18\u7684\u78b1\u57fa\u5927\u90e8\u5206\u662f\u4f4e\u8d28\u91cf\u78b1\u57fa\uff0c\u8865\u6d1e\u65f6\u9700\u8981\u5148\u5c06gap\u8fb9\u7f18\u8be5\u6570\u76ee\u7684\u78b1\u57fatrim\u6389\uff0c\u4f5c\u4e3aN\u5904\u7406\u3002<br \/>\n-i default:10 \u8fed\u4ee3\u7684\u6700\u5927\u6b21\u6570\u3002<br \/>\n-g default:1 \u4f7f\u7528bowtie\u8fdb\u884c\u6bd4\u5bf9\u7684\u65f6\u5019\u5141\u8bb8\u7684\u6700\u5927\u7684gap\u6570\uff0c\u548cbowtie\u4e2d\u7684-v\u53c2\u6570\u4e00\u81f4<br \/>\n-T default:1 \u8fd0\u884c\u65f6\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570<br \/>\n-S \u8df3\u8fc7\u91cd\u65b0\u8bfb\u53d6\u8f93\u5165\u6587\u4ef6<br \/>\n-b \u8f93\u51fa\u6587\u4ef6\u7684basename\u3002<\/code><\/p>\n<p>-l \u53c2\u6570\u6240\u6307\u5411\u7684library\u6587\u4ef6\u9700\u8981\u5148\u884c\u7f16\u8f91\u597d\u3002\u8be5\u6587\u4ef6\u5305\u542b7\u5217\uff0c\u6bcf\u4e00\u5217\u4e4b\u95f4\u4ee5\u7a7a\u683c(space)\u9694\u5f00.\u5176\u4f8b\u5b50\u548c\u683c\u5f0f\u5982\u4e0b\uff1a<\/p>\n<pre>\r\nLib1 bwa file1.1.fasta file1.2.fasta 400 0.25 FR \r\nLib1 bowtie file2.1.fasta file2.2.fasta 400 0.25 FR \r\nLib2 bowtie file3.1.fastq file3.2.fastq 4000 0.5 RF\r\n<\/pre>\n<p><code>\u7b2c1\u5217\uff1alibrary\u540d\u79f0<br \/>\n\u7b2c2\u5217\uff1a\u4f7f\u7528\u7684\u5e8f\u5217\u6bd4\u5bf9\u65b9\u6cd5\uff0c\u5982\u679creads\u957f\u5ea6<50,\u5219\u4f7f\u7528bowtie\uff1b\u82e5\u957f\u5ea6>50\u5e76<150,\u5219\u4f7f\u7528bwa\uff1b\u82e5\u957f\u5ea6\u5f88\u5927\uff0c\u6bd4\u5982454\u7684reads\uff0c\u5219\u4f7f\u7528bwa\u3002BWA\u548cBWA-sw\u8fd0\u884c\u5728\u9ed8\u8ba4\u6a21\u5f0f\u4e0b\u3002\n\u7b2c3,4\u5217\uff1a\u53cc\u672b\u7aef\u6d4b\u5e8f\u7684fastq\u6587\u4ef6\u6216fasta\u6587\u4ef6\u3002\n\u7b2c5,6\u5217\uff1a\u63d2\u5165\u7247\u6bb5\u7684\u957f\u5ea6\uff0c\u4ee5\u53ca\u627f\u8ba4\u7684\u957f\u5ea6\u3002\u6bd4\u5982\u4e0a\u4f8b\u5b50\u4e2d\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u4e3a400bp\uff0c\u6210\u5bf9\u7684reads\u7684\u7247\u6bb5\u957f\u5ea6\u53ea\u6709\u5728[400-400*0.25,400+400*0.25]\u8303\u56f4\u5185\u624d\u88ab\u627f\u8ba4\u3002\n\u7b2c7\u5217\uff1a\u53cc\u7aef\u6d4b\u5e8freads\u7684\u65b9\u5411\uff0c\u6709FF\uff0cFR\uff0cRF\u548cRR\u51e0\u79cd\u3002<\/code><\/p>\n<h1>4. \u4f8b\u5b50<\/h1>\n<p>\u7f16\u8f91\u4e00\u4e2alibraries.txt\u6587\u4ef6\uff0c\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n<pre>\r\nIllumina_160bp bwa fragment.reads1.fastq fragment.reads2.fastq 156 0.25 FR\r\nIllumina_6000bp bwa jumping.reads1.fastq jumping.reads2.fastq 6170 0.25 FR\r\n<\/pre>\n<p>\u8fd0\u884cGapFiller\u7a0b\u5e8f\uff0c\u5982\u4e0b\uff1a<\/p>\n<pre>\r\n$GapFillerHome\/GapFiller.pl -l libraries.txt\\\r\n  -s genome.fasta -m 90 -T 8 -b species\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. GapFiller\u7b80\u4ecb \u7ec4\u88c5\u51fa\u6765\u7684\u57fa\u56e0\u7ec4\u8349\u56fe\u7684scaffold\u9700\u8981\u8fdb\u4e00\u6b65\u8fdb &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1733\">\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":[3],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1733"}],"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=1733"}],"version-history":[{"count":12,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1733\/revisions"}],"predecessor-version":[{"id":1735,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1733\/revisions\/1735"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1733"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1733"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1733"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}