{"id":1702,"date":"2013-06-19T20:46:38","date_gmt":"2013-06-19T12:46:38","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1702"},"modified":"2013-06-21T01:02:35","modified_gmt":"2013-06-20T17:02:35","slug":"ngs%e6%95%b0%e6%8d%ae%e7%9a%84error-correction%e6%96%b9%e6%b3%95","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1702","title":{"rendered":"NGS\u6570\u636e\u7684Error correction\u65b9\u6cd5"},"content":{"rendered":"

\u53c2\u8003\u81ea\u6587\u732e\uff1aYang X,Chockalingam SP,Aluru S. A survey of error-correction methods for next-generation sequencing. Brief. Bioinformatics 2013;14:56-66.<\/a>\u3002<\/p>\n

\u73b0\u5728\u8fdb\u884cerror-correciton\u7684\u7b97\u6cd5\u6709\u4e09\u79cd\uff1a k-spectrum-based\u3001Suffix tree\/array based \u548c MSA based\u3002\u672c\u6587\u5bf9\u4ee5\u4e0b\u8f6f\u4ef6\u4f7f\u7528\u771f\u5b9e\u6570\u636e\u8fdb\u884c\u4e86\u8bc4\u4f30\uff1aHSHREC\u3001Reptile\u3001Quake\u3001SOAPec\u3001HiTEC\u3001ECHO\u3001Coral\uff08\u53ea\u6709\u7b2c\u4e00\u4e2a\u548c\u6700\u540e\u4e00\u4e2a\uff0c\u51712\u4e2a\u8f6f\u4ef6\u7528\u4e8e454\u548cion\u6570\u636e\u7684\u8bc4\u4f30\uff1b\u6240\u6709\u8f6f\u4ef6\u90fd\u7528\u4e8e\u4e86Illumina\u6570\u636e\u7684\u8bc4\u4f30\uff09\u3002<\/p>\n

\u8be5\u6587\u732e\u7684\u7ed3\u679c\u8868\u660e\uff1a\u9002\u7528\u4e8eIllumina\u6570\u636e\u7684\u8f6f\u4ef6(\u6211\u4e2a\u4eba\u8ba4\u4e3a\u7684\u4f18\u5148\u987a\u5e8f)\u662f Reptile\u3001HiTEC(\u57282*100\u7684\u6570\u636e\u4e2d\u7ed3\u679c\u6700\u597d) \u548c ECHO\u3002Reptile\u7684\u53c2\u6570\u9009\u62e9\u6bd4\u5176\u5b83\u4e24\u4e2a\u8f6f\u4ef6\u8981\u9ebb\u70e6\u5f88\u591a\uff1bHiTEC\u4e0d\u9002\u5408\u5904\u7406\u6709\u2018N\u2019\u7684\u6216\u4e0d\u540c\u957f\u5ea6reads\u3002\u9002\u7528\u4e8e454\u548cion\u6570\u636e\u7684\u8f6f\u4ef6\u662fCoral\u3002<\/p>\n

\u4ee5\u4e0a\u662f\u5bf9\u57fa\u56e0\u7ec4\u7684\u6d4b\u5e8freads\u8fdb\u884c\u4fee\u6b63\u7684\u65b9\u6cd5\uff0c\u800c\u65b0\u51fa\u4e86\u4e00\u4e2a\u5bf9RNA-Seq\u6570\u636e\u8fdb\u884c\u4fee\u6b63\u7684\u8f6f\u4ef6\uff1aSEECER\u3002\u5176\u6587\u732e\u4e3a\uff1aProbabilistic error correction for RNA sequencing<\/a>\u3002\u6587\u4e2d\u7ed3\u679c\u8868\u793a\uff0c\u4ee5\u4e0a\u5bf9\u57fa\u56e0\u7ec4reads\u8fdb\u884c\u4fee\u6b63\u7684\u65b9\u6cd5\u5bf9RNA-Seq reads\u7684\u4fee\u6b63\u6548\u679c\u4e0d\u597d\u3002<\/p>\n

\u4ee5\u4e0b\u662f\u8fd9\u51e0\u4e2a\u8f6f\u4ef6\u7684\u5b89\u88c5\u4e0e\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n

1. HiTEC<\/h1>\n

HiTEC\u7684\u4e0b\u8f7d\u7f51\u9875\uff1ahttp:\/\/www.csd.uwo.ca\/~ilie\/HiTEC\/<\/a>\u3002\u6839\u636e\u5176\u5b89\u88c5\u6e90\u7801\u5305\u5185\u7684\u8bf4\u660e\u6587\u4ef6\uff0cHiTEC\u7684\u5b89\u88c5\u9700\u8981\u5148\u884c\u5b89\u88c5gsl library,\u7136\u540e\u4fee\u6539Makefile\u6587\u4ef6\uff0c\u6700\u540e\u8fdb\u884cmake\u3002<\/p>\n

HiTEC\u7684\u53c2\u6570\u6bd4\u8f83\u7b80\u5355\uff0c\u8fd0\u884c\u65b9\u6cd5\u5982\u4e0b\uff1a<\/p>\n

\r\n$ .\/hitec <inputReads> <correctedReads> \\\r\n  <GenomeLength> <per-base error rate>\r\n\r\n$ .\/hitec S.aureusReads.fasta \\\r\nS.aureusCorrectedReads.fasta 2820462 1\r\n<\/pre>\n
\u8f93\u5165fasta\u6216fastq\u6587\u4ef6\uff0c\u7ed9\u5b9a\u4e00\u4e2a\u5927\u81f4\u7684\u57fa\u56e0\u7ec4\u5927\u5c0f\u548c\u78b1\u57fa\u9519\u8bef\u7387\uff0c\u5219\u4f1a\u8fd0\u884c\uff0c\u5e76\u5c06\u7ed3\u679c\u8f93\u51fa\u5230\u6307\u5b9a\u6587\u4ef6\u4e2d\u3002<\/p>\n
HiTEC\u5c06\u5ffd\u7565\u90a3\u4e9b\u542b\u6709\u78b1\u57fa \u201cN\u201d \u7684reads\uff0c\u8fd9\u4e9breds\u4e0d\u4f1a\u5728\u8f93\u51fa\u6587\u4ef6\u4e2d\u663e\u793a\u3002\u8f93\u51fa\u7ed3\u679c\u4e3afasta\u6587\u4ef6\uff0cfasta\u7684\u5934\u88ab\u66f4\u6362\u4e86\uff0c\u53d8\u6210\u4e86\u4ece0\u5f00\u59cb\u7684\u6570\u5b57\u3002<\/p>\n
2. ECHO<\/h1>\n
ECHO\u7684\u4e0b\u8f7d\u7f51\u9875\uff1ahttp:\/\/uc-echo.sourceforge.net\/<\/a>\u3002\u6839\u636e\u5176\u5b89\u88c5\u6e90\u7801\u5305\u5185\u7684\u8bf4\u660e\u6587\u4ef6\uff0cECHO\u7684\u5b89\u88c5\u9700\u8981\u6709GCC\uff0cPython\uff0cSciPy\u548cNumPy\uff0c\u4f7f\u7528yum\u5b89\u88c5\u5373\u53ef\u3002ECHO\u7684\u8fd0\u884c\u4e5f\u6bd4\u8f83\u7b80\u5355\uff1a<\/p>\n
\r\n$ python ErrorCorrection.py -b 2000000 --nh 256 \\\r\n  --ncpu 6 -o output\/5Mreads.fastq 5Mreads.fastq\r\n<\/pre>\n
\u751f\u6210\u4e86\u7ed3\u679c\u6587\u4ef6\u548cHiTEC\u4e00\u6837\uff0c\u751f\u6210fasta\u6587\u4ef6\uff0cfasta\u7684\u5934\u88ab\u66f4\u6362\u4e86\uff0c\u53d8\u6210\u4e86\u4ece0\u5f00\u59cb\u7684\u6570\u5b57\u3002<\/p>\n
3. reptile<\/h1>\n
reptile\u7684\u4e0b\u8f7d\u7f51\u9875\uff1ahttp:\/\/aluru-sun.ece.iastate.edu\/doku.php?id=reptile<\/a>\u3002<\/p>\n
reptile\u7684\u4f7f\u7528\u8bf4\u660e\u76f8\u6bd4\u524d\u4e24\u4e2a\u8f6f\u4ef6\uff0c\u66f4\u52a0\u5b8c\u6574\u3002\u5176\u4f7f\u7528\u8bf4\u660e\u53c2\u8003\u8f6f\u4ef6\u5305\u4e2d\u7684readme\u6587\u4ef6\u548c\u7f51\u9875\u7684turorial<\/a>\u3002\u4ee5\u4e0b\u4e3areptile\u4f7f\u7528\u5b9e\u4f8b\uff1a<\/p>\n
3.1 \u5c06fastq\u6587\u4ef6\u8f6c\u6362\u6210fa\u6587\u4ef6\u548cq\u6587\u4ef6<\/h1>\n
\u5bf9\u8c61\u4e3a\u540d\u4e3areads.fastq\u7684\u6587\u4ef6\uff0c\u4f4d\u4e8e\u5f53\u524d\u5de5\u4f5c\u76ee\u5f55\u3002reads.fastq\u4e3a\u4f7f\u7528NGSQC-toolkit\u8fc7\u6ee4\u6389\u4f4e\u8d28\u91cfreads\u548c\u542b\u6709N\u7684reads\u540e\u7684\u6587\u4ef6\u3002<\/p>\n
\r\n$ $reptileHome\/utils\/fastq-converter-v2.0.pl .\/ .\/ 1\r\n<\/pre>\n
\u7ed3\u679c\u751f\u6210reads.fa\u548creads.q\u6587\u4ef6\u3002\u8fd9\u4e24\u4e2a\u6587\u4ef6\u90fd\u4e3afast\u683c\u5f0f\uff0cfasta\u5934\u4e3a\u4ece0\u5f00\u59cb\u6309\u987a\u5e8f\u6392\u5217\u7684\u6570\u5b57\uff0c\u5185\u5bb9\u5206\u522b\u4e3a\u5e8f\u5217\u548c\u8d28\u91cf\u3002<\/p>\n
3.2 seq-analy\u914d\u7f6e\u6587\u4ef6\u53c2\u6570\u8c03\u6574<\/h2>\n
copy\u4e00\u4e2a\u8303\u672c\u7684seq-analy\u914d\u7f6e\u6587\u4ef6\u548cReptile\u914d\u7f6e\u6587\u4ef6\u3002<\/p>\n
\r\n$ cp $reptileHome\/utils\/seq-analy\/config-example seq-analy-config\r\n$ cp $reptileHome\/src\/config-example reptile-config\r\n<\/pre>\n
\u5c06\u8be5\u914d\u7f6e\u6587\u4ef6\u4fee\u6539\u5982\u4e0b\uff1a<\/p>\n
\r\nIFlag                   1\r\nBatchSize               1000000\r\nInFaFile                .\/reads.fa\r\nIQFile                  .\/reads.q\r\nKmerLen                 24\r\nOKmerHistFile           .\/kmerhist\r\nQHistFile               .\/qualhist\r\nOKmerCntFile    \r\nMaxErrRate              0.02\r\nQThreshold              73\r\nMaxBadQPerKmer          4\r\nQFlag                   1\r\n<\/pre>\n
\u4fee\u6539\u597d\u8f93\u5165\u548c\u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u540e\uff0c\u8fd0\u884c\u7a0b\u5e8f\uff1a<\/p>\n
\r\n$ $reptileHome\/utils\/seq-analy\/seq-analy seq-analy-config\r\n<\/pre>\n
\u4ee5\u4e0a\u547d\u4ee4\u6267\u884c\u540e\u751f\u6210\u6839\u636e\u914d\u7f6e\u6587\u4ef6\u4fe1\u606f\u8f93\u51fa.\/kmerhist\u548c.\/qualhist\u4e24\u4e2a\u6587\u4ef6\u3002<\/p>\n
\u7ee7\u7eed\u4fee\u6539seq-analy-config\u914d\u7f6e\u6587\u4ef6\u4fe1\u606f\uff1a
\n1. reads\u957f\u5ea6\u4e3a35bp\u7684\u65f6\u5019\uff0cMaxBadQPerKmer\u7684\u503c\u8bbe\u4e3a4-6\uff1breads\u957f\u5ea6\u4e3a100+bp\u7684\u65f6\u5019\uff0cMaxBadQPerKmer\u7684\u503c\u8bbe\u4e3a6-10.
\n2. KmerLen\u53ef\u4ee5\u6309\u81ea\u5df1\u7684\u610f\u613f\u8bbe\u7f6e\uff0c\u53ef\u4ee5\u4fdd\u7559\u4e3a\u9ed8\u8ba4\u768424.
\n3. \u67e5\u770b.\/qualhist\u6587\u4ef6\u4fe1\u606f\uff0c\u627e\u51fa\u7b2c\u4e09\u5217\u7d2f\u8ba1\u9891\u7387 >=0.8 \u7684\u90a3\u4e00\u884c\u5bf9\u5e94\u7684\u78b1\u57fa\u8d28\u91cf\u5bf9\u5e94\u7684ASCII\u503c\uff0c\u4f5c\u4e3aQThreshold\u7684\u503c\uff1b\u540c\u65f6\u627e\u51fa\u7b2c\u4e09\u5217\u7d2f\u8ba1\u9891\u7387 <= 0.2 \u7684\u90a3\u4e00\u884c\u5bf9\u5e94\u7684\u78b1\u57fa\u8d28\u91cf\u5bf9\u5e94\u7684ASCII\u503c\uff0c\u4f5c\u4e3a\u4e0b\u4e00\u6b65 Reptile\u914d\u7f6e\u6587\u4ef6\u4e2d Qlb \u53c2\u6570\u7684\u503c\u3002\n\n\u4fee\u6539\u5b8cseq-analy-config\u914d\u7f6e\u6587\u4ef6\u540e\uff0c\u7ee7\u7eed\u8fd0\u884c\u201cseq-analy seq-analy-config\u201d\uff0c\u76f4\u5230\u4e0d\u7528\u7ee7\u7eed\u4fee\u6539\u4e3a\u6b62\uff1b\u5982\u679c\u5f53\u524d\u4e0d\u7528\u4fee\u6539\uff0c\u5219\u8fdb\u5165\u4e0b\u4e00\u6b65\u3002\n\n\n
3.3 Reptile\u914d\u7f6e\u6587\u4ef6\u53c2\u6570\u8c03\u6574<\/h2>\n
\u5bf9\u8303\u672cReptile\u914d\u7f6e\u6587\u4ef6\u4fee\u6539\uff0c\u4fee\u6539\u8bfb\u53d6\u6587\u4ef6\u548c\u8f93\u51fa\u6587\u4ef6\uff0c\u5982\u4e0b\uff1a<\/p>\n
\r\nInFaFile                .\/reads.fa\r\nQFlag                   1\r\nIQFile                  .\/reads.q\r\nOErrFile                .\/reads.errors\r\nBatchSize               1000000 \r\nKmerLen                 12\r\nhd_max                  1\r\nStep                    12\r\nExpectSearch            16 \r\nT_ratio                 0.5\r\n\r\n######## The following parameters need to be tuned to specific dataset ########\r\n\r\nQThreshold              73\r\nMaxBadQPerKmer          4\r\nQlb                     62\r\nT_expGoodCnt            16\r\nT_card                  6\r\n<\/pre>\n
\u901a\u65f6\uff0c\u5bf9\u4e0a\u6570\u7684\u4e00\u4e9b\u53c2\u6570\u8fdb\u884c\u4fee\u6539\uff1a
\n1. T_expGoodCnt\uff0c\u8bbe\u7f6e\u4e3a.\/kmerhist\u7b2c\u4e09\u5217\u7d2f\u8ba1\u9891\u7387\u6700\u63a5\u8fd10.95\u7684\u4e00\u884c\u7684\u7b2c\u4e00\u5217\u7684\u503c\u76842\u500d\uff1b
\n2. T_card\uff0c\u8bbe\u7f6e\u4e3a.\/kmerhist\u7b2c\u4e8c\u5217\u4e2d\u7b2c\u4e8c\u5927\u7684\u503c\u7684\u4e00\u884c\u6240\u5bf9\u5e94\u7684\u7b2c\u4e00\u5217\u7684\u503c\uff1b
\n3. KmerLen\uff0c\u8bbe\u7f6e\u4e3a >= (seq-analy\u6700\u7ec8\u7684\u914d\u7f6e\u6587\u4ef6\u4e2d\u8be5\u53c2\u6570\u7684\u503c\u7684\u4e00\u534a);
\n4. QThreshold, \u548cseq-analy\u6700\u7ec8\u7684\u914d\u7f6e\u6587\u4ef6\u4e2d\u8be5\u503c\u7684\u8bbe\u7f6e\u4e00\u81f4\uff1b
\n5. Qlb\uff0c \u8bbe\u7f6e\u4e3a.\/qualhist\u6587\u4ef6\u4e2d\uff0c\u7b2c\u4e09\u5217\u7d2f\u8ba1\u9891\u7387 <= 0.2 \u7684\u90a3\u4e00\u884c\u5bf9\u5e94\u7684\u78b1\u57fa\u8d28\u91cf\u5bf9\u5e94\u7684ASCII\u503c\uff1b\n6. MaxBadQPerKmer\uff0c\u548cseq-analy\u6700\u7ec8\u7684\u914d\u7f6e\u6587\u4ef6\u4e2d\u8be5\u503c\u7684\u8bbe\u7f6e\u4e00\u81f4\uff1b\n7. step  \u8bbe\u7f6e\u4e3a\u3010\uff08seq-analy\u6700\u7ec8\u7684\u914d\u7f6e\u6587\u4ef6\u4e2dKmerLen\u503c\uff09 - (\u672creptile\u53c2\u6570\u6587\u4ef6\u4e2dKmerLen\u7684\u503c)\u3011\u7684\u503c\n\n\n
3.4 \u8fd0\u884cReptile<\/h2>\n
\r\n$ $reptileHome\/src\/reptile-v1.1 reptile-config\r\n<\/pre>\n
\u751f\u6210\u4e86\u914d\u7f6e\u6587\u4ef6\u4e2d\u8bbe\u5b9a\u7684\u7ed3\u679c\u6587\u4ef6.\/reads.errors\u3002\u8be5\u6587\u4ef6\u683c\u5f0f\u4e3a\uff1a<\/p>\n
 ReadID    ErrNum    [pos to from qual]    [pos to from qual] …<\/p>\n
\u7b2c\u4e00\u5217\u662fread ID; \u7b2c\u4e8c\u5217\u4e3a\u8be5read\u9519\u8bef\u7684\u78b1\u57fa\u6570; \u5bf9\u6bcf\u4e00\u4e2a\u9519\u8bef\u7684\u78b1\u57fa\uff0c\u67094\u4e2a\u503c\u7ed9\u51fa\u6765\uff1a\u8be5\u9519\u8bef\u78b1\u57fa\u7684\u4f4d\u7f6e(pos)\u3001\u65b0\u7684\u4fee\u6b63\u540e\u7684\u78b1\u57fa(to)\u3001\u539f\u6765\u7684\u9519\u8bef\u7684\u78b1\u57fa(from) \u548c \u8be5\u4f4d\u70b9\u78b1\u57fa\u8d28\u91cf\u5bf9\u5e94\u7684ASCII\u503c(qual)\u3002<\/p>\n
3.5 \u751f\u6210\u4fee\u6b63\u540e\u7684fasta\u6587\u4ef6<\/h2>\n
\r\n$ $reptileHome\/utils\/reptile_merger\/reptile_merger \\\r\n  .\/reads.fa .\/reads.errors out.fa\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
\u53c2\u8003\u81ea\u6587\u732e\uff1aYang X,Chockalingam SP,Aluru S. A  … \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":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1702"}],"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=1702"}],"version-history":[{"count":14,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1702\/revisions"}],"predecessor-version":[{"id":1716,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1702\/revisions\/1716"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1702"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1702"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1702"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}