{"id":2329,"date":"2015-08-25T16:59:33","date_gmt":"2015-08-25T08:59:33","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2329"},"modified":"2015-08-25T16:59:33","modified_gmt":"2015-08-25T08:59:33","slug":"%e4%bd%bf%e7%94%a8-reapr-%e8%bf%9b%e8%a1%8c%e5%9f%ba%e5%9b%a0%e7%bb%84%e9%94%99%e8%af%af%e8%af%84%e4%bc%b0","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2329","title":{"rendered":"\u4f7f\u7528 REAPR \u8fdb\u884c\u57fa\u56e0\u7ec4\u9519\u8bef\u8bc4\u4f30"},"content":{"rendered":"<h1>1. REAPR \u7b80\u4ecb<\/h1>\n<p>REAPR(Recognition of Errors in Assemblies using Paired Reads)\u80fd\u5229\u7528\u6210\u5bf9\u7684reads\u6765\u8bc6\u522b\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e2d\u7684\u9519\u8bef\u3002\u4ece\u800c\uff0c\u80fd\u5c06\u57fa\u56e0\u7ec4\u5e8f\u5217\u4ece\u9519\u8bef\u7684gap\u5904\u65ad\u5f00\u6216\u5c06\u9519\u8bef\u5e8f\u5217\u4f7f\u7528 Ns \u4ee3\u66ff\u3002\u540c\u65f6\uff0c\u5bf9\u9519\u8bef\u4fe1\u606f\u8fdb\u884c\u7edf\u8ba1\u3002<\/p>\n<h1>2. REAPR\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n<p>REAPR\u5b98\u7f51\uff1a<a href=\"http:\/\/www.sanger.ac.uk\/resources\/software\/reapr\/\" target=\"_blank\">http:\/\/www.sanger.ac.uk\/resources\/software\/reapr\/<\/a><br \/>\n\u5b89\u88c5 REAPR \u9700\u8981\u5148\u5b89\u88c5 R \u548c Perl \u6a21\u5757\uff1a File::Basename, File::Copy, File::Spec, File::Spec::Link, Getopt::Long, List::Util\u3002<\/p>\n<pre>\r\n$ wget ftp:\/\/ftp.sanger.ac.uk\/pub\/resources\/software\/reapr\/Reapr_1.0.17.tar.gz\r\n$ tar zxf Reapr_1.0.17.tar.gz -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/Reapr_1.0.17\r\n$ wget ftp:\/\/ftp.sanger.ac.uk\/pub\/resources\/software\/reapr\/Reapr_1.0.17.manual.pdf\r\n$ .\/install.sh\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/Reapr_1.0.17' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n\r\n\u6d4b\u8bd5Reapr\u80fd\u5426\u6b63\u5e38\u8fd0\u884c\uff1a\r\n$ wget ftp:\/\/ftp.sanger.ac.uk\/pub4\/resources\/software\/reapr\/Reapr_1.0.17.test_data.tar.gz\r\n$ tar zxf Reapr_1.0.17.test_data.tar.gz \r\n$ .\/test.sh\r\n<\/pre>\n<h1>3. REAPR \u4f7f\u7528<\/h1>\n<p>reapr \u6700\u5c11\u9700\u8981\u8f93\u5165\u57fa\u56e0\u7ec4fasta\u6587\u4ef6\u548cmate-pair\u6570\u636e\uff08\u9700\u8981\u5c06RF\u65b9\u5411\u8f6c\u53d8\u6210FR\u65b9\u5411\uff09\u6587\u4ef6\u3002\u5e38\u7528\u7684\u8fd0\u884c\u6b65\u9aa4\u5982\u4e0b\uff1a<\/p>\n<pre>\r\n\u4f7f\u7528 facheck \u547d\u4ee4\u68c0\u67e5\u57fa\u56e0\u7ec4fasta\u6587\u4ef6\uff0c\u4ee5\u9632fasta\u6587\u4ef6\u5e8f\u5217\u540d\u542b\u6709\u602a\u5f02\u5b57\u7b26\u3002\r\n$ reapr facheck genome.fasta\r\n\u4f7f\u7528\u4e0b\u5217\u547d\u4ee4\u5bf9fasta\u6587\u4ef6\u8fdb\u884c\u4fee\u6539\u3002\r\n$ reapr facheck genome.fasta new_genome.fasta\r\n\r\n\u4f7f\u7528SMALT\u5c06 mate-pair reads\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u4e0a\u3002\r\n$ reapr smaltmap genome.fasta jumping.1.fastq jumping.2.fastq jumping.bam\r\n\r\n\u8fd0\u884creapr pipeline\u5bf9\u57fa\u56e0\u7ec4\u8fdb\u884c\u8bc4\u4f30\u3002\u5c06\u7ed3\u679c\u8f93\u51fa\u5230 outdir \u6587\u4ef6\u5939\u4e2d\u3002\r\n$ reapr pipeline genome.fasta jumping.bam outdir\r\n<\/pre>\n<p>reapr \u4e5f\u652f\u6301\u8f93\u5165paired-end\u6570\u636e(\u53ef\u9009)\u3002\u901a\u8fc7\u5c06paired-end\u6570\u636euniquely\u5e76perfecly\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\uff0c\u4ece\u800c\u80fd\u8ba1\u7b97\u51fa\u57fa\u56e0\u7ec4\u4e0aerror-free\u7684\u78b1\u57fa\u4f4d\u70b9\u5e76\u8fdb\u884c\u7edf\u8ba1\u3002\u8be5\u9879\u76ee\u5206\u6790\u5bf9error calling\u6ca1\u6709\u5f71\u54cd\u3002\u503c\u5f97\u6ce8\u610f\u7684\u662f\uff1a \u9ed8\u8ba4\u8bbe\u7f6e\u4e0bcall\u4e00\u4e2aerror-free\u4f4d\u70b9\u9700\u8981\u81f3\u5c115x\u7684\u8986\u76d6\u5ea6\uff1b\u540c\u65f6\u8f93\u5165\u7684paired-end\u6570\u636e\u7684\u65b9\u5411\u8981\u4e3ainward(\u4e00\u822cpaired-end\u6570\u636e\u65b9\u5411\u5373\u4e3ainward)\uff0c\u6b64\u5916reapr\u4ec5\u652f\u6301inward\u65b9\u5411\uff0c\u56e0\u6b64\u8f93\u5165\u7684jumping\u6570\u636e\u4e5f\u8981\u5148\u8f6c\u6362\u4e3ainward\u65b9\u5411\u3002<\/p>\n<p>\u4f7f\u7528paired-end\u6570\u636e\u7684\u547d\u4ee4\u884c\uff1a<\/p>\n<pre>\r\n$ reapr smaltmap genome.fasta jumping.1.fastq jumping.2.fastq jumping.bam\r\n$ reapr perfectmap genome.fasta frag.1.fastq frag.2.fastq insert_size perfect_prefix\r\n$ reapr pipeline genome.fasta jumping.bam outdir perfect_prefix\r\n<\/pre>\n<p>reapr\u7684\u8fd0\u884c\u6d41\u7a0b\uff1a<br \/>\n<img src=\"http:\/\/www.chenlianfu.com\/data\/pictures\/reapr_pipeline.png\" alt=\"reapr_pipeline\" \/><\/p>\n<h1>4. reapr\u7684\u7ed3\u679c<\/h1>\n<p>REAPR \u4f1a\u5bf9\u57fa\u56e0\u7ec4\u6bcf\u4e2a\u4f4d\u70b9\u7684 FCD(fragment coverage distribution)\u8fdb\u884c\u5206\u6790\u3002\u671f\u671b\u7684FCD\u548c\u5b9e\u9645\u4e0a\u7684\u4e0aFCD\u4e4b\u5dee\u4e3a&#8221;FCD error&#8221;\u3002 FCD error\u5f80\u5f80\u4ee3\u8868\u4e0d\u6b63\u786e\u7684scaffold\u8fde\u63a5\u3001\u5927\u7684\u63d2\u5165\u7f3a\u5931\u6216contig\u5e8f\u5217\u4e2d\u4e0d\u6b63\u786e\u7684\u8fde\u63a5\u3002\u4e3a\u4e86\u80fd\u66f4\u597d\u5730\u8ba1\u7b97FCD\uff0c\u7279\u522b\u662fgap\u4f4d\u70b9\u7684FCD\uff0cmate-pair\u6570\u636e\u7684insert size\u8d8a\u5927\u8d8a\u597d\u3002<\/p>\n<p>REAPR\u5bf9\u8f93\u5165\u7684paired reads\u6570\u636e\u8fdb\u884c\u68c0\u6d4b\uff0c\u5e76\u5c06\u7ed3\u679c\u653e\u5165\u5230\u6587\u4ef6\u5939 outdir\/00.Sample\/ \u4e0b\u3002<\/p>\n<pre>\r\ngc_vs_cov.lowess.pdf: GC\u504f\u597d\u6027\u68c0\u6d4b\u56fe\r\ninsert.in.pdf: FR(inner\/inward)\u7c7b\u578b\u63d2\u5165\u7247\u6bb5\u7684\u957f\u5ea6\u68c0\u6d4b\u56fe\r\ninsert.out.pdf: RF\u7c7b\u578b\u63d2\u5165\u7247\u6bb5\u7684\u957f\u5ea6\u68c0\u6d4b\u56fe\r\ninsert.stats.txt: \u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u7edf\u8ba1\r\n<\/pre>\n<p>\u4ece\u9519\u8bef\u4f4d\u70b9\u6253\u65ad\u540e\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\uff1a outdir\/04.break.broken assembly.fa \u3002<br \/>\n\u5982\u679cFCD error\u533a\u6709gap\uff0c\u5219\u4ecegap\u5904\u5c06\u57fa\u56e0\u7ec4\u5e8f\u5217\u6253\u65ad\uff1b\u82e5FCD error\u533a\u6ca1\u6709gap\uff0c\u5219\u5c06\u5176\u7528Ns\u4ee3\u66ff\u3002\u540c\u65f6\u5c06\u88ab\u4ee3\u66ff\u7684\u5e8f\u5217\u5199\u5165\u5230\u6587\u4ef6 outdir\/04.break.broken assembly bin.fa\u4e2d\u3002<\/p>\n<p>\u57fa\u56e0\u7ec4\u9519\u8bef\u7edf\u8ba1\u6587\u4ef6\uff1a outdir\/05.summary.report.txt\u3002\u8be5\u6587\u4ef6\u7edf\u8ba1\u4f4d\u4e8e contig \u4e2d\u7684 FCD error \u7684\u6570\u76ee\uff0c\u548c\u542b\u6709 gap \u7684 FCD error \u7684\u6570\u76ee\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. REAPR \u7b80\u4ecb REAPR(Recognition of Errors  &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2329\">\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":[39,40],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2329"}],"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=2329"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2329\/revisions"}],"predecessor-version":[{"id":2330,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2329\/revisions\/2330"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2329"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2329"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2329"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}