{"id":2146,"date":"2014-06-11T03:00:20","date_gmt":"2014-06-10T19:00:20","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2146"},"modified":"2014-06-11T04:06:25","modified_gmt":"2014-06-10T20:06:25","slug":"%e4%bd%bf%e7%94%a8-icorn-%e8%bf%9b%e8%a1%8c%e5%9f%ba%e5%9b%a0%e7%bb%84%e6%a0%b8%e8%8b%b7%e9%85%b8%e7%9a%84%e4%bf%ae%e6%ad%a3","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2146","title":{"rendered":"\u4f7f\u7528 ICORN \u8fdb\u884c\u57fa\u56e0\u7ec4\u6838\u82f7\u9178\u7684\u4fee\u6b63"},"content":{"rendered":"

1. ICORN \u7b80\u4ecb<\/h1>\n

ICORN (Iterative Correction Of Reference Nucleotides), \u80fd\u901a\u8fc7\u5c06 reads \u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\uff0c\u4ece\u800c\u4fee\u6b63 SNP \u548c \u5c0f\u4e8e 3bp \u7684 INDEL \u4f4d\u70b9\u3002\u73b0\u5728\u51fa\u4e86\u65b0\u7684\u7248\u672c ICORN2 \u3002
\nICORN \u5b98\u7f51\uff1a http:\/\/icorn.sourceforge.net\/<\/a>
\nICORN \u53c2\u8003\u6587\u732e\uff1a Otto T D, Sanders M, Berriman M, et al. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology[J]. Bioinformatics, 2010, 26(14): 1704-1707.<\/a><\/p>\n

2. ICORN \u539f\u7406<\/h1>\n

ICORN \u7684\u539f\u7406\u5982\u4e0b\u56fe\u6240\u793a\u3002ICORN2 \u8c03\u7528 SMALT \u5c06 reads map \u5230\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e0a\uff1b\u7136\u540e Call SNPs \u548c <=3bp INDELs\uff1b\u6839\u636e\u5176\u4f4d\u70b9\u7684\u8986\u76d6\u5ea6\u60c5\u51b5\u51b3\u5b9a\u57fa\u56e0\u7ec4\u4e0a\u8be5\u4f4d\u70b9\u7684\u6838\u82f7\u9178\u7c7b\u578b\u3002\u6700\u540e\u901a\u8fc7\u591a\u8f6e\u8fed\u4ee3\u76f4\u5230\u4e0d\u80fd call \u5230\u65b0\u7684 variants \u4e3a\u6b62\u3002\n\"http:\/\/icorn.sourceforge.net\/workflow.jpg\"<\/p>\n

3. ICORN \u7684\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n

ICORN \u7684\u4f7f\u7528\u4f1a\u8c03\u7528\u7b2c\u4e09\u65b9\u7684\u8f6f\u4ef6\uff1a GATK\u3001SMALT\u3001samtools \u548c SNP-o-AMTIC \u3002<\/p>\n

\r\n$ wget ftp:\/\/ftp.sanger.ac.uk\/pub4\/resources\/software\/pagit\/ICORN2\/icorn2.V0.95.tgz\r\n$ tar zxf icorn2.V0.95.tgz -C \/opt\/biosoft\/\r\n$ \/opt\/biosoft\/ICORN2\/icorn2.sh --help\r\n<\/pre>\n
4. ICORN \u7684\u4f7f\u7528<\/h1>\n
4.1 \u4f7f\u7528\u524d\u51c6\u5907<\/h2>\n
\u51c6\u5907\u7684\u8f93\u5165\u6587\u4ef6\u662f\uff1a readroot_1.fastq\u3001readroot_2.fastq\u3001genome.fasta\uff0c\u5c06\u8fd93\u4e2a\u6587\u4ef6\u653e\u7f6e\u4e8e\u5de5\u4f5c\u76ee\u5f55\u4e2d\u3002
\n\u540c\u65f6\uff0c\u9700\u8981\u7ed9\u4e00\u4e9b\u73af\u5883\u53d8\u91cf\u8d4b\u503c\uff1a<\/p>\n
\r\n\u8bbe\u5b9a\u7a0b\u5e8f\u6240\u5728\u7684\u76ee\u5f55\r\n$ export ICORN2_HOME=\/opt\/biosoft\/ICORN2\/\r\n\u8bbe\u5b9a\u8fd0\u884c\u7684\u7ebf\u7a0b\u6570\r\n$ export ICORN2_THREADS=24\r\n\u8bbe\u5b9a\u8f93\u51fa\u4fe1\u606f\u7684\u591a\u6216\u5c11,\u5bf9 debug \u6709\u7528\r\n$ export ICORN2_VERBOSE=2\r\n<\/pre>\n
4.2 \u8fd0\u884c\u8f6f\u4ef6<\/h2\u300b\n\n\n
\r\n$ \/opt\/biosoft\/ICORN2\/icorn2.sh readroot 350 genome.fasta 1 3\r\n<\/pre>\n
\u4ee5\u4e0a\u547d\u4ee4\u7b2c 2 \u4e2a\u53c2\u6570\u662f\u6570\u636e\u7684 insert size\uff1b 1 \u548c 3 \u4ee3\u8868\u8fed\u4ee3\u7684\u8d77\u59cb\u548c\u7ec8\u6b62\uff0c\u8868\u793a\u8fed\u4ee3 3 \u6b21\u3002\u5982\u679c\u9700\u8981\u7ee7\u7eed\u8fed\u4ee3\uff0c\u5219\u8bbe\u7f6e\u8d77\u59cb\u4e3a 4 \u3002\u4e0a\u8ff0\u7a0b\u5e8f\u7684\u7ed3\u679c\u6587\u4ef6\u4e3a ICORN2.Query.contigs.fa.4 \u3002\u5728 ICORN2_3 \u6587\u4ef6\u5939\u4e2d\u4e5f\u542b\u6709\u8be5 fasta \u6587\u4ef6\uff0c\u540c\u65f6\u7a0b\u5e8f\u4e5f\u751f\u6210\u4e86\u4e00\u4e2a gff \u6587\u4ef6\u3002\u4f5c\u8005\u63a8\u8350\u5c06\u8fd9\u4e24\u4e2a\u6587\u4ef6\u8f7d\u5165\u5230 artemis <\/a>\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u4e2d\u8fdb\u884c\u67e5\u770b\u3002<\/p>\n
5. \u601d\u8003<\/h1>\n
\u6709\u4e9b\u4eba\u5728\u6709\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u72b6\u51b5\u4e0b\u505a\u4e86\u91cd\u6d4b\u5e8f\uff0c\u603b\u662f\u60f3\u8981\u5f97\u5230\u5176\u91cd\u6d4b\u5e8f\u7684\u57fa\u56e0\u7ec4\u7ed3\u679c\u3002\u53ef\u4ee5\u4f7f\u7528 ICORN \u5bf9\u53c2\u8003\u57fa\u56e0\u7ec4\u8fdb\u884c\u4fee\u6b63\uff0c\u5373\u5f97\u5230\u4e86\u5bf9\u5e94\u5176\u54c1\u79cd\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
1. ICORN \u7b80\u4ecb ICORN (Iterative Correction  … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2146"}],"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=2146"}],"version-history":[{"count":11,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2146\/revisions"}],"predecessor-version":[{"id":2157,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2146\/revisions\/2157"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2146"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2146"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2146"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}