{"id":719,"date":"2013-03-20T09:07:30","date_gmt":"2013-03-20T01:07:30","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=719"},"modified":"2013-06-17T09:31:20","modified_gmt":"2013-06-17T01:31:20","slug":"allpath-lg%e7%9a%84%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=719","title":{"rendered":"ALLPATHS-LG\u7684\u4f7f\u7528"},"content":{"rendered":"<h1>\u4e00\u3001ALLPATH\u7b80\u4ecb<\/h1>\n<p><a href=\"http:\/\/www.broadinstitute.org\/software\/allpaths-lg\/blog\/\" title=\"AllPaths-LG\u5b98\u7f51\" target=\"_blank\">ALLPATHS-LG<\/a>\u662f\u4e00\u4e2a\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\uff0c\u9002\u5408\u4e8e\u7ec4\u88c5short reads\u6570\u636e\uff0c\u7531Computational Research and Development group at the Broad Institute\u5f00\u53d1\u3002ALLPATHS-LG\u662f\u73b0\u5728\u884c\u4e1a\u5185\u516c\u8ba4\u8fdb\u884c\u57fa\u56e0\u7ec4<em>De novo<\/em>\u7ec4\u88c5\u6548\u679c\u6700\u597d\u7684\u8f6f\u4ef6\u3002<\/p>\n<h1>\u4e8c. <a href=\"http:\/\/www.broadinstitute.org\/software\/allpaths-lg\/blog\/?page_id=215\">\u57fa\u7840\u6ce8\u610f\u4e8b\u9879<\/a><\/h1>\n<pre>1. \u4e0d\u80fd\u53ea\u4f7f\u7528\u4e00\u4e2alibrary\u6570\u636e\u8fdb\u884c\u7ec4\u88c5\uff1b\r\n2. \u5fc5\u987b\u6709\u4e00\u4e2a\"overlapping\"\u7684\u7247\u6bb5\u6587\u5e93\u7684paired-reads\u6570\u636e\u3002\u6bd4\u5982\uff0creads\u957f\u5ea6~\r\n100bp\uff0c\u63d2\u5165\u7247\u6bb5\u5e93\u957f\u5ea6~180bp;\r\n3. \u5fc5\u987b\u6709jumping library\u6570\u636e\uff1b\r\n4. \u57fa\u56e0\u7ec4\u7ec4\u88c5\u9700\u8981100x\u6216\u4ee5\u4e0a\u57fa\u56e0\u7ec4\u8986\u76d6\u5ea6\u7684\u78b1\u57fa\uff0c\u8fd9\u4e2a\u8986\u76d6\u5ea6\u662f\u6307raw reads\u6570\u636e(\u5728\r\nerror correction\u548cfiltering\u4e4b\u524d)\u7684\u8986\u76d6\u5ea6\uff1b\r\n5. \u53ef\u4ee5\u4f7f\u7528PacBio\u6570\u636e\uff1b\r\n6. \u4e0d\u80fd\u4f7f\u7528454\u6570\u636e\u548cTorrent\u6570\u636e\u3002\u4e3b\u8981\u662f\u8fd9\u4e24\u8005\u6d4b\u5e8f\u592a\u8d35\uff0c\u5982\u679c\u4ec0\u4e48\u65f6\u5019\u4ef7\u683c\u964d\u4f4e\uff0c\u6709\r\n\u9700\u6c42\u7684\u8bdd\uff0c\u4f1a\u5199\u51fa\u76f8\u5e94\u7684\u4ee3\u7801\u6765\u6ee1\u8db3\u8981\u6c42\uff1b\r\n7. \u5b98\u65b9\u63d0\u4f9b\u4e86<a href=\"ftp:\/\/ftp.broadinstitute.org\/pub\/crd\/ALLPATHS\/Release-LG\/\">\u6d4b\u8bd5\u7528\u6570\u636e<\/a>\uff1b\r\n8. \u4e0d\u652f\u6301\u5728\u6574\u4e2a\u8ba1\u7b97\u673a\u96c6\u7fa4\u4e0a\u8fdb\u884c\u8fd0\u7b97\uff1b\r\n9. \u9700\u8981\u6d88\u8017\u7684\u5185\u5b58\u5cf0\u503c\u5927\u7ea6\u662f1.7bytes\u6bcf\u4e2a\u78b1\u57fa\uff0c\u5373\u8f93\u516510G\u7684\u78b1\u57fa\u6570\u636e\u91cf\uff0c\u5927\u7ea6\u9700\u898117\r\nG\u5185\u5b58\uff1b\r\n10. \u5bf9\u4e8e\u8bd5\u63a2\u6027\u7684\u53c2\u6570\uff0c\u6bd4\u5982K\uff0c\u539f\u5219\u4e0a\u53ef\u4ee5\u8c03\u6574\u3002\u4f46\u662f\u6211\u4eec\u4e0d\u4f1a\u81ea\u884c\u8c03\u6574\uff0c\u5e76\u4e5f\u4e0d\u63a8\u8350\u3002AL\r\nLPATHS-LG\u4e0d\u50cf\u5176\u5b83<em>De novo<\/em>\u4e00\u6837\uff0cKmer\u5927\u5c0f\u7684\u53c2\u6570K\u548cread\u5927\u5c0f\u4e4b\u95f4\u6ca1\u6709\u76f4\u63a5\u7684\u8054\u7cfb\uff0c\r\nALLPATHS-LG\u4f1a\u5728\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u8fd0\u7528\u4e00\u7cfb\u5217\u7684K\u503c\u3002<\/pre>\n<h1>\u4e09. ALLPATHS-LG\u4f7f\u7528\u65b9\u6cd5<\/h1>\n<h2>1. \u57fa\u7840\u7684\u4f7f\u7528\u65b9\u6cd5\u548c\u547d\u4ee4<\/h2>\n<p>\u4f7f\u7528RunAllPathsLG\u8fd9\u4e2a\u547d\u4ee4\u6765\u8fd0\u884c\u3002\u867d\u7136\u6709\u5f88\u591a\u53c2\u6570\uff0c\u4f46\u662f\u5728\u6ca1\u6709\u6307\u5bfc\u7684\u60c5\u51b5\u4e0b\u4e0d\u8981\u968f\u610f\u4f7f\u7528\uff0c\u4f7f\u7528\u9ed8\u8ba4\u8bbe\u7f6e\u5373\u53ef\u3002\u5176\u4f7f\u7528\u65b9\u6cd5\u4e3a\uff1a<\/p>\n<pre>$ RunAllPathsLG arg1=value1 arg2=value2 ...<\/pre>\n<p>\u53c2\u6570\u4e3b\u8981\u662f\u8bbe\u7f6e\u7a0b\u5e8f\u8fa8\u522b\u7684\u4e00\u4e9b\u76ee\u5f55\uff0c\u5728\u7a0b\u5e8f\u7684\u8fd0\u884c\u8fc7\u7a0b\uff0c\u4f1a\u8f93\u5165\u76f8\u5e94\u76ee\u5f55\u4e2d\u7684\u6570\u636e\uff0c\u5c06\u7ed3\u679c\u8f93\u5165\u5230\u6307\u5b9a\u7684\u76ee\u5f55\u3002\u4e00\u4e2a\u7b80\u5355\u7684\u547d\u4ee4\u4f7f\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>#!\/bin\/sh\r\n\r\n# ALLPATHS-LG needs 100 MB of stack space.  In 'csh' run 'limit stacksize 100000'.\r\nulimit -s 100000\r\n# ALLPATHS-LG\u547d\u4ee4\u7684\u5199\u6cd5\u4e0e\u4e00\u822c\u7684linux\u53c2\u6570\u5199\u6cd5\u4e0d\u662f\u5f88\u4e00\u6837\u3002\u91c7\u7528 \u2018\u53c2\u6570=\u503c\u2019 \u7684\u65b9\u6cd5\uff0c\u5e76\u4f7f\u4e4b\u6210\u6bcf\u884c\u4e00\u4e2a\u53c2\u6570\uff0c\u4f7f\u7528'\\'\u6765\u8fde\u63a5\u5404\u4e2a\u53c2\u6570\uff0c\u8fd9\u6837\u770b\u8d77\u6765\u76f4\u89c2\u6613\u61c2\u3002\u521d\u59cb\u63a5\u89e6\u7684\u4eba\u53ef\u80fd\u4f1a\u4e0d\u9002\u5e94\u3002\r\n\r\nRunAllPathsLG \\\r\n PRE=$PWD\\\r\n REFERENCE_NAME=species.genome\\\r\n DATA_SUBDIR=data\\\r\n RUN=run\\\r\n SUBDIR=test\\\r\n EVALUATION=STANDARD\\\r\n TARGETS=standard\\\r\n OVERWRITE=True\\\r\n MAXPAR=8\r\n | tee -a assemble.out<\/pre>\n<h2>2. \u8be6\u7ec6\u7684\u53c2\u6570\u8bf4\u660e<\/h2>\n<pre>\u5fc5\u987b\u7684\u53c2\u6570\r\n<span style=\"color: #ff00ff;\">PRE (String)<\/span>\r\n    \u7a0b\u5e8f\u8fd0\u884c\u7684\u6839\u76ee\u5f55\uff0c\u6240\u6709\u7684\u5176\u5b83\u76ee\u5f55\u5168\u5728\u8be5\u76ee\u5f55\u4e0b\r\n<span style=\"color: #ff00ff;\">REFERENCE_NAME (String)<\/span>\r\n    \u53c2\u8003\u57fa\u56e0\u7ec4\u76ee\u5f55\u540d\u79f0\uff0c\u4f4d\u4e8ePRE\u76ee\u5f55\u4e0b\u3002\u5982\u679c\u6709\u4e00\u4e2a\u53c2\u8003\u57fa\u56e0\u7ec4\uff0c\u53ef\u5c06\u53c2\u8003\u57fa\u56e0\u7ec4\u653e\u5230\u8be5\r\n\u76ee\u5f55\u4e2d\uff1b\u82e5\u6ca1\u6709\uff0c\u5219\u521b\u5efa\u8be5\u6587\u4ef6\u5939\u7528\u4e8e\u57fa\u56e0\u7ec4\u7ec4\u88c5\r\n<span style=\"color: #ff00ff;\">DATA_SUBDIR (String)<\/span>\r\n    DATA\u5b50\u76ee\u5f55\u540d\u79f0\uff0c\u4f4d\u4e8eREFERENCE_NAME\u76ee\u5f55\u4e0b\u3002\u7a0b\u5e8f\u4ece\u8be5\u76ee\u5f55\u4e2d\u8bfb\u53d6\u6570\u636e\u3002\r\n<span style=\"color: #ff00ff;\">RUN (String)<\/span>\r\n    \u8fd0\u884c\u76ee\u5f55\u540d\u79f0\uff0c\u4f4d\u4e8eDATA_SUBDIR\u4e0b\u3002\u7a0b\u5e8f\u5c06\u751f\u6210\u7684\u4e2d\u95f4\u6587\u4ef6\u548c\u7ed3\u679c\u6587\u4ef6\u5b58\u50a8\u4e8e\u8be5\u76ee\u5f55\r\n\u3002\u6bd4\u5982\u7ec4\u88c5\u7ed3\u679c\u662f\u4e00\u4e2a\u540d\u4e3aASSEMBLES\u7684\u76ee\u5f55\uff0c\u4f4d\u4e8e\u8be5\u76ee\u5f55\u4e0b\u3002\r\n\r\n\u90e8\u5206\u53ef\u9009\u53c2\u6570\uff1a\r\n<span style=\"color: #ff00ff;\">SUBDIR (String) default: test<\/span>\r\n    \u5b50\u76ee\u5f55\u540d\uff0c\u5728REF\/DATA\/RUN\/ASSEMBLIES\u76ee\u5f55\u4e0b\u521b\u5efa\u7684\u5b58\u653e\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\u7684\u76ee\u5f55\r\n\u540d\u3002\r\n<span style=\"color: #ff00ff;\">K (int) default: 96<\/span>\r\n    \u6838\u5fc3Kmer\u5927\u5c0f\uff0c\u53ea\u6709K=96\u80fd\u5f88\u597d\u5730\u8fd0\u884c\u3002\r\n<span style=\"color: #ff00ff;\">EVALUATION (String: {NONE,BASIC,STANDARD,FULL,CHEAT})default:BASIC<\/span>\r\n    \u7ed9\u5b9a\u4e00\u4e2a\u53c2\u8003\u57fa\u56e0\u7ec4\uff0cpipeline\u80fd\u5728\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7684\u4e0d\u540c\u9636\u6bb5\u5bf9\u7ec4\u88c5\u8fc7\u7a0b\u548c\u7ed3\u679c\u8fdb\u884c\u8bc4\u4f30\u3002\r\n    BASIC:\u57fa\u7840\u8bc4\u4f30\uff0c\u4e0d\u9700\u8981\u53c2\u8003\u57fa\u56e0\u7ec4\uff1b\r\n    STANDARD:\u4f7f\u7528\u53c2\u8003\u57fa\u56e0\u7ec4\u6765\u8fd0\u884c\u8bc4\u4f30\u6a21\u5757\uff1b\r\n    FULL:\u5728\u67d0\u4e9b\u7ec4\u88c5\u6a21\u5757\u4e0b\u6253\u5f00in-place\u8bc4\u4f30\uff0c\u4e0d\u4f1a\u5f71\u54cd\u7ec4\u88c5\u7ed3\u679c\uff1b\r\n    CHEAT:\u7a0d\u5fae\u4f7f\u7528\u53c2\u8003\u57fa\u56e0\u7ec4\u6307\u5bfc\u7ec4\u88c5\uff0c\u4ea7\u751f\u66f4\u8be6\u7ec6\u7684\u5206\u6790\uff0c\u80fd\u5bf9\u7ec4\u88c5\u7ed3\u679c\u4ea7\u751f\u5c0f\u7684(\u597d\u65b9\r\n\u5411\u7684)\u6539\u53d8\u3002\r\n<span style=\"color: #ff00ff;\">REFERENCE_FASTA (String) default: REF\/genome.fasta<\/span>\r\n    \u8bc4\u4f30\u4e2d\u4f7f\u7528\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u3002\r\n<span style=\"color: #ff00ff;\">MAXPAR (int) default: 1<\/span> \r\n    \u6709\u4e9b\u6a21\u5757\u7684\u8fd0\u884c\u662f\u72ec\u7acb\u7684\uff0c\u4e0d\u76f8\u4e92\u4f9d\u8d56\uff0c\u80fd\u540c\u65f6\u8fd0\u884c\u3002\u8be5\u53c2\u6570\u8bbe\u5b9a\u80fd\u540c\u65f6\u8fd0\u884c\u7684\u6a21\u5757\u7684\u6700\r\n\u5927\u6570\u76ee\u3002\u7531\u4e8epipeline\u4e2d\u7684\u7edd\u5927\u90e8\u5206\u6a21\u5757\u90fd\u80fd\u591a\u7ebf\u7a0b\u8fd0\u884c\uff0c\u56e0\u6b64\u5c06\u8be5\u503c\u8bbe\u5b9a\u5927\u4e8e1\uff0c\u6548\u679c\u4e0d\u660e\r\n\u663e\u3002\r\n<span style=\"color: #ff00ff;\">THREADS (String) default: max<\/span> \r\n    \u6709\u4e9b\u6a21\u5757\u80fd\u591a\u7ebf\u7a0b\u7a0b\u8fd0\u884c\uff0c\u9ed8\u8ba4\u4f7f\u7528\u6700\u5927\u7ebf\u7a0b\u6570\u8fd0\u884c\u3002\r\n<span style=\"color: #ff00ff;\">OVERWRITE (Bool) default: False<\/span> \r\n    \u662f\u5426\u8986\u76d6\u5b58\u5728\u7684\u6587\u4ef6\u3002\u53ef\u4ee5\u8bbe\u7f6e\u8be5\u9009\u9879\u4e3aTrue\uff0c\u5728\u6bcf\u6b21\u8fd0\u884c\u7a0b\u5e8f\u7684\u65f6\u5019\u8bbe\u5b9aRUN\u53c2\u6570\u4e3a\r\n\u4e00\u4e2a\u65b0\u7684\u76ee\u5f55\u540d\uff0c\u5219\u6bd4\u8f83\u597d\u3002\r\n<span style=\"color: #ff00ff;\">TARGETS (vec) default: standard<\/span> \r\n    pipeline\u4f1a\u751f\u6210\u4e00\u7cfb\u5217\u7684\u6587\u4ef6\uff0c\u4e0d\u540c\u7684\u6587\u4ef6\u7684\u751f\u6210\u9700\u8981call\u4e0d\u540c\u7684\u6a21\u5757\u3002\u5982\u679c\u67d0\u6587\u4ef6\r\n\u5df2\u7ecf\u5b58\u5728\u4e86\u5e76\u4e14\u662f\u6700\u65b0\u7684\uff0c\u5219\u8df3\u8fc7\u76f8\u5e94\u7684\u6a21\u5757\u7684\u8fd0\u884c\u3002\u672c\u53c2\u6570\u6307\u5b9a\u751f\u6210\u54ea\u4e9b\u62df\u5b9a\u7684\u76ee\u6807\u6587\u4ef6(p\r\nseudo targets)\u3002\u82e5\u76ee\u6807\u6587\u4ef6\u6ca1\u6709\u76f8\u5e94\u7684\u6a21\u5757\u80fd\u751f\u6210\uff0c\u5219\u4f1a\u5f97\u5230\u62a5\u9519\u3002\r\n    none:\u6ca1\u6709\u62df\u5b9a\u7684\u76ee\u6807\u6587\u4ef6\uff0c\u4ec5\u4ec5\u751f\u6210\u6307\u5b9a\u7684\u76ee\u6807\u6587\u4ef6\uff1b\r\n    standard:\u751f\u6210\u7ec4\u88c5\u6587\u4ef6\u548c\u9009\u5b9a\u7684\u8bc4\u4f30\u6587\u4ef6\uff1b\r\n    full_eval:\u751f\u6210\u7ec4\u88c5\u6587\u4ef6\u548c\u989d\u5916\u7684\u8bc4\u4f30\u6587\u4ef6\u3002\r\n<span style=\"color: #ff00ff;\">TARGETS_REF (String)<\/span> \r\n    \u5728ref_dir\u76ee\u5f55\u4e2d\u751f\u6210\u7684\u76ee\u6807\u6587\u4ef6\u3002\r\n    \u591a\u4e2a\u76ee\u6807\u6587\u4ef6\u7684\u4e66\u5199\u65b9\u6cd5\u4e3a\uff1a TARGETS_REF=\"{target1,target2,target3}\" \u3002\r\n<span style=\"color: #ff00ff;\">TARGETS_DATA (String)<\/span> \r\n    \u5728data\u76ee\u5f55\u4e2d\u751f\u6210\u7684\u76ee\u6807\u6587\u4ef6\u3002\r\n<span style=\"color: #ff00ff;\">TARGETS_RUN (String)<\/span> \r\n    \u5728run\u76ee\u5f55\u4e2d\u751f\u6210\u7684\u76ee\u6807\u6587\u4ef6\u3002\r\n<span style=\"color: #ff00ff;\">TARGETS_SUBDIR (String)<\/span>\r\n    \u5728subdir\u4e2d\u751f\u6210\u7684\u76ee\u6807\u6587\u4ef6\u3002 \r\n<span style=\"color: #ff00ff;\">FORCE_TARGETS (Bool) default: False<\/span>\r\n    \u751f\u6210\u76ee\u6807\u6587\u4ef6\uff0c\u5373\u4f7f\u6587\u4ef6\u5df2\u7ecf\u5b58\u5728\u5e76\u4e14\u770b\u8d77\u6765\u662f\u5f88\u65b0\u7684\u3002<\/pre>\n<h2>3. \u8f93\u5165\u6587\u4ef6\u4e0e\u76ee\u5f55\u7684\u51c6\u5907<\/h2>\n<p>\u4e24\u4e2a\u6587\u5e93\uff1a\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u4e3a180bp\u548c3000bp\uff0cillumina\u6d4b\u5e8f\u6587\u4ef6\u7ed3\u679c\u4e3afastq\u683c\u5f0f\u3002\u4ee5\u6b64\u4e3a\u4f8b\u6765\u51c6\u5907ALLPATHS-LG\u8fd0\u884c\u6240\u9700\u7684\u6587\u4ef6\u548c\u76ee\u5f55\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">(1) \u51c6\u5907 in_groups.csv \u548c in_libs.csv \u6587\u4ef6\u3002<\/span><\/p>\n<p>\u8fd9\u4e24\u4e2a\u6587\u4ef6\u5185\u5bb9\u7531\u9017\u53f7\u9694\u5f00\uff0cin_groups.csv\u6587\u4ef6\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n<pre>group_name, library_name, file_name\r\nfirest, Illumina_180bp, seq\/species_500bp_read?.fastq\r\nsecond, Illumina_3000bp, seq\/species_3000bp_read?.fastq<\/pre>\n<p>in_groups.csv\u6587\u4ef6\u7684\u89e3\u91ca\uff1a<\/p>\n<pre>group_name:\u6570\u636e\u72ec\u7279\u7684\u4ee3\u53f7,\u6bcf\u4e00\u4efd\u6570\u636e\u6709\u4e00\u4e2a\u4ee3\u53f7\uff1b\r\nlibrary_name:\u6570\u636e\u6240\u5c5e\u6587\u5e93\u7684\u540d\u5b57\uff0c\u4f53\u73b0\u51fa\u8be5\uff1b\r\nfilename:\u6570\u636e\u6587\u4ef6\u6240\u5b58\u653e\u4f4d\u7f6e\u3002\u53ef\u4ee5\u4e3a\u76f8\u5bf9\u4f4d\u7f6e\uff0c\u6587\u4ef6\u540d\u53ef\u4ee5\u5305\u542b'*'\u548c'?'(\u4f46\u662f\u6269\u5c55\u540d\r\n\u4e2d\u4e0d\u80fd\u6709\u8be5\u7b26\u53f7\uff0c\u56e0\u4e3a\u8981\u6839\u636e\u6269\u5c55\u540d\u8bc6\u522b\u6587\u4ef6\u7c7b\u578b)\uff0c\u4ece\u800c\u4ee3\u8868paired\u6570\u636e\u3002\u652f\u6301\u7684\u6587\u4ef6\u7c7b\u578b\u6709\r\n'.bam','fasta','fa','fastq','fq','fastq.gz'\u548c'fq.gz'\u3002<\/pre>\n<p>in_libs.csv\u6587\u4ef6\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n<pre>library_name, project_name, organism_name, type, paired, frag_size, frag_stddev, insert_size, insert_stddev, read_orientation, genomic_start, genomic_end\r\nIllumina_180bp, species, species.genome, fragment, 1, 180, 10, , , inward, 0, 0\r\nIllumina_3000bp, species, species.genome, jumping, 1, , , 3000, 500, outward, 0, 0<\/pre>\n<p>in_libs.csv\u6587\u4ef6\u7684\u89e3\u91ca\uff1a<\/p>\n<pre>library_name:\u548cin_groups.csv\u4e2d\u7684\u76f8\u5339\u914d\uff1b\r\nproject_name:project\u7684\u540d\u5b57\uff1b\r\norganism_name:\u6d4b\u5e8f\u7269\u79cd\u7684\u540d\u5b57\uff1b\r\ntype:\u4ec5\u4ec5\u53ea\u662f\u4e00\u4e2a\u4fe1\u606f\uff1b\r\npaired:0:Unpaired reads;1:paired reads;\r\nfrag_size:\u5c0f\u7247\u6bb5\u6587\u5e93\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u7684\u5747\u503c\uff1b\r\nfrag_stddev:\u5c0f\u7247\u6bb5\u6587\u5e93\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u4f30\u7b97\u7684\u6807\u51c6\u504f\u5dee\uff1b\r\ninsert_size:\u5927\u7247\u6bb5\u6587\u5e93\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u7684\u5747\u503c\uff1b\r\ninsert_stddev:\u5927\u7247\u6bb5\u6587\u5e93\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u4f30\u7b97\u7684\u6807\u51c6\u504f\u5dee\uff1b\r\nread_orientation:reads\u7684\u65b9\u5411\uff0c\u5c0f\u7247\u6bb5\u6587\u5e93\u4e3ainward\uff0c\u5927\u7247\u6bb5\u6587\u5e93\u4e3aoutward\uff1b\r\ngenomic_start:reads\u4ece\u8be5\u4f4d\u7f6e\u5f00\u59cb\uff0c\u8bfb\u5165\u6570\u636e\uff0c\u5982\u679c\u4e0d\u4e3a0\uff0c\u4e4b\u524d\u7684\u78b1\u57fa\u90fd\u88ab\u526a\u6389\uff1b\r\ngenomic_end:reads\u4ece\u8be5\u4f4d\u7f6e\u5f00\u59cb\uff0c\u505c\u6b62\u8bfb\u5165\u6570\u636e\uff0c\u5982\u679c\u4e0d\u4e3a0\uff0c\u4e4b\u540e\u7684\u78b1\u57fa\u90fd\u88ab\u526a\u6389\u3002<\/pre>\n<p><span style=\"color: #ff00ff;\">(2) \u4f7f\u7528PrepareAllPathsInputs.pl\u6765\u5bf9\u6570\u636e\u8fdb\u884c\u8f6c\u6362<\/span><\/p>\n<p>ALLPATHS-LG\u63a5\u53d7\u7684\u8f93\u5165\u6570\u636e\u8981\u6c42\u5982\u4e0b\uff1a<\/p>\n<pre>1. ALLPATHS-LG\u7684\u8f93\u5165\u6570\u636e\u652f\u6301\u5c0f\u7247\u6bb5\u6587\u5e93(fragment library)\u3001\u5927\u7247\u6bb5\u6587\u5e93(jum\r\nping library)\u548c\u8d85\u5927\u7247\u6bb5\u6587\u5e93(long jumping library)\u3002\u5e76\u4e14\u524d\u4e24\u79cd\u6587\u5e93\u81f3\u5c11\u5404\u6709\r\n\u4e00\u4e2a\u624d\u80fd\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5\u3002\u8d85\u5927\u7247\u6bb5\u6587\u5e93\u662f\u53ea\u63d2\u5165\u7247\u6bb5&gt;20kb\u7684\u6587\u5e93\uff0c\u5176\u6d4b\u5e8f\u65b9\u5411\u548c\u5c0f\u7247\u6bb5\u6587\r\n\u5e93\u4e00\u81f4\uff0c\u4e3ainward\u3002\r\n\r\n2. ALLPATHS-LG\u7684\u8f93\u5165\u6570\u636e\u653e\u7f6e\u5728\/\/\u6587\u4ef6\u5939\u4e0b\uff0c\u5305\u542b3\u79cd\u6587\u4ef6\uff1a\u78b1\u57fa\u6587\u4ef6\uff0c\u8d28\u91cf\u6587\u4ef6\u548c\u914d\r\n\u5bf9\u4fe1\u606f\u6587\u4ef6\r\n   frag_reads_orig.fastb\r\n   frag_reads_orig.qualb \r\n   frag_reads_orig.pairs \r\n\r\n   jump_reads_orig.fastb \r\n   jump_reads_orig.qualb \r\n   jump_reads_orig.pairs\r\n\r\n\u4ee5\u4e0b\u662f\u53ef\u9009\u7684\u8d85\u5927\u63d2\u5165\u7247\u6bb5\u6587\u5e93\u5bf9\u5e94\u7684\u6570\u636e\u6587\u4ef6\uff08\u975e\u5fc5\u987b\uff09\uff1a\r\n\r\n  long_jump_reads_orig.fastb \r\n  long_jump_reads_orig.qualb \r\n  long_jump_reads_orig.pairs<\/pre>\n<p>\u4f7f\u7528PrepareAllPathsInputs.pl\u6765\u5c06fastq\u7b49\u683c\u5f0f\u7684\u6d4b\u5e8f\u7ed3\u679c\u8f6c\u6362\u6210ALLPATHS-LG\u53ef\u63a5\u53d7\u7684\u6587\u4ef6\u3002\u4ee5\u4e0b\u662f\u8be5\u7a0b\u5e8f\u7684\u53c2\u6570\uff1a<\/p>\n<pre><span style=\"color: #ff00ff;\">DATA_DIR<\/span>\r\n    \u5c06\u8f6c\u6362\u540e\u7684\u6570\u636e\u6587\u4ef6\u653e\u5230\u6b64\u6587\u4ef6\u5939\u4e0b\u3002\r\n<span style=\"color: #ff00ff;\">PICARD_TOOLS_DIR<\/span>\r\n    \u82e5\u8f93\u5165\u6570\u636e\u4e3abam\u683c\u5f0f\uff0c\u5219\u9700\u8981\u7528\u5230Picard\u8f6f\u4ef6\uff0c\u8be5\u53c2\u6570Picard\u7684\u8def\u5f84\r\n<span style=\"color: #ff00ff;\">IN_GROUPS_CSV<\/span>\r\n    \u8f93\u5165\u7684in_groups.csv\u6587\u4ef6\u540d\r\n<span style=\"color: #ff00ff;\">IN_LIBS_CSV<\/span>\r\n    \u8f93\u5165\u7684in_libs.csv\u6587\u4ef6\u540d\r\n<span style=\"color: #ff00ff;\">INCLUDE_NON_PF_READS default: 1<\/span>\r\n    1:\u5305\u542bnon-PF reads\uff1b0:\u4ec5\u4ec5\u53ea\u5305\u542bPF reads.\r\n<span style=\"color: #ff00ff;\">PHRED_64 default: 0<\/span>\r\n    0:\u78b1\u57fa\u8d28\u91cf\u662fASCII\u768433\u5230126\uff0c\u4e00\u822c\u60c5\u51b5\u4e0bIllumina\u6570\u636e\u7684\u6700\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f'B';\r\n1:\u78b1\u57fa\u8d28\u91cf\u7684ASCII\u7801\u662f\u4ece64\u5230126\uff0c\u4e00\u822c\u60c5\u51b5\u4e0bIllumina\u6570\u636e\u7684\u6700\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f'#'\u3002\r\nPLOIDY\r\n    \u751f\u6210ploidy\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u5c31\u5305\u542b\u4e00\u4e2a\u6570\u5b57 1 \u6216\u8005 2 \u30021\u8868\u793a\u57fa\u56e0\u7ec4\u4e3a\u5355\u500d\u4f53\u578b\uff0c2\u8868\r\n\u793a\u53cc\u500d\u4f53\u578b\u3002\r\n<span style=\"color: #ff00ff;\">HOSTS<\/span>\r\n    \u5217\u51fa\u5e73\u884cforking\u7684host\u4e3b\u673a(\u8fd9\u4e9b\u4e3b\u673a\u5fc5\u987b\u8981\u80fd\u65e0\u5bc6\u7801\u76f4\u63a5ssh\u8fde\u4e0a)\u3002\u6bd4\u5982\u201c2,3.\r\nhost2,4.host3\"\u8868\u793a\u4f7f\u7528\u672c\u5730\u673a\u5668\u76842\u4e2aCPU\u7ebf\u7a0b\uff0chost2\u673a\u5668\u76843\u4e2aCPU\u7ebf\u7a0b\u548chost3\u673a\r\n\u5668\u76844\u4e2aCPU\u7ebf\u7a0b\u3002\r\n\r\n\u4ee5\u4e0b\u662f\u4e0d\u5e38\u7528\u7684\u53c2\u6570\uff0c\u4e3b\u8981\u7528\u6765\u9009\u62e9\u8f6c\u6362\u7684\u6570\u636e\u91cf\u7684\u5927\u5c0f\u3002\u5f53\u6d4b\u5e8f\u6570\u636e\u91cf\u592a\u591a\uff0c\u800c\u53ea\u60f3\u4f7f\u7528\u5176\r\n\u4e2d\u4e00\u90e8\u5206\u6570\u636e\u7684\u65f6\u5019\uff0c\u53ef\u4ee5\u7528\u5230\r\n<span style=\"color: #ff00ff;\">FRAG_FRAC<\/span>\r\n    \u4f7f\u7528\u5c0f\u7247\u6bb5\u5e93reads\u7684\u6bd4\u4f8b\u3002\u6bd4\u5982 30% \u6216 0.3 \u3002\u5982\u679c\u8bbe\u5b9a\u4e86\u6b64\u503c\uff0c\u5219\u4e0d\u80fd\u540c\u65f6\u8bbe\u5b9a\r\nFRAG_COVERAGE\u3002\r\n<span style=\"color: #ff00ff;\">JUMP_FRAC<\/span>\r\n    \u4f7f\u7528\u5927\u7247\u6bb5\u5e93reads\u7684\u6bd4\u4f8b\u3002\u6bd4\u5982 20% \u6216 0.2 \u3002\u5982\u679c\u8bbe\u5b9a\u4e86\u6b64\u503c\uff0c\u5219\u4e0d\u80fd\u540c\u65f6\u8bbe\u5b9a\r\nJUMP_COVERAGE\u3002\r\n<span style=\"color: #ff00ff;\">LONG_JUMP_FRAC<\/span>\r\n    \u4f7f\u7528\u8d85\u5927\u7247\u6bb5\u5e93reads\u7684\u6bd4\u4f8b\u3002 \u6bd4\u5982 90% \u6216 0.9 \u3002\u5982\u679c\u8bbe\u5b9a\u4e86\u6b64\u503c\uff0c\u5219\u4e0d\u80fd\u540c\u65f6\r\n\u8bbe\u5b9aLONG_JUMP_COVERAGE\u3002\r\n<span style=\"color: #ff00ff;\">GENOME_SIZE<\/span>\r\n    \u4f30\u8ba1\u7684\u57fa\u56e0\u7ec4\u5927\u5c0f\uff0c\u7528\u6765\u8ba1\u7b97\u5bf9\u5e94\u8986\u76d6\u5ea6\u6240\u5bf9\u5e94\u7684reads\u6570\r\n<span style=\"color: #ff00ff;\">FRAG_COVERAGE<\/span>\r\n    \u6240\u671f\u671b\u7684\u5c0f\u7247\u5ea6\u5e93\u7684\u8986\u76d6\u5ea6\uff0c\u6bd4\u5982 45. \u8981\u6c42GENOME_SIZE\u6709\u8bbe\u5b9a\r\n<span style=\"color: #ff00ff;\">JUMP_COVERAGE<\/span>\r\n    \u6240\u671f\u671b\u7684\u5927\u7247\u5ea6\u5e93\u7684\u8986\u76d6\u5ea6\uff0c\u6bd4\u5982 45. \u8981\u6c42GENOME_SIZE\u6709\u8bbe\u5b9a\r\n<span style=\"color: #ff00ff;\">LONG_JUMP_COVERAGE<\/span>\r\n    \u6240\u671f\u671b\u7684\u8d85\u5927\u7247\u5ea6\u5e93\u7684\u8986\u76d6\u5ea6\uff0c\u6bd4\u5982 1. \u8981\u6c42GENOME_SIZE\u6709\u8bbe\u5b9a<\/pre>\n<p>\u4e00\u4e2a\u00a0PrepareAllPathsInputs.pl \u7684\u4f8b\u5b50\u5982\u4e0b\uff1a<\/p>\n<pre>#!\/bin\/sh\r\n\r\n# ALLPATHS-LG needs 100 MB of stack space.  In 'csh' run 'limit stacksize 100000'.\r\nulimit -s 100000\r\n\r\nmkdir -p species.genome\/data\r\n\r\n# NOTE: The option GENOME_SIZE is OPTIONAL. \r\n#       It is useful when combined with FRAG_COVERAGE and JUMP_COVERAGE \r\n#       to downsample data sets.\r\n#       By itself it enables the computation of coverage in the data sets \r\n#       reported in the last table at the end of the preparation step. \r\n\r\n# NOTE: If your data is in BAM format you must specify the path to your \r\n#       picard tools bin directory with the option: \r\n#\r\n#       PICARD_TOOLS_DIR=\/your\/picard\/tools\/bin\r\n\r\nPrepareAllPathsInputs.pl\\\r\n DATA_DIR=$PWD\/species.genome\/data\\\r\n PLOIDY=1\\\r\n IN_GROUPS_CSV=in_groups.csv\\\r\n IN_LIBS_CSV=in_libs.csv\\\r\n OVERWRITE=True\\\r\n | tee prepare.out<\/pre>\n<p><span style=\"color: #ff00ff;\">(3) \u4f7f\u7528Fasta2Fastb\u6765\u8f6c\u6362\u5f97\u5230\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u8f93\u5165\u6570\u636e<\/span><\/p>\n<p>\u5c06\u53c2\u8003\u57fa\u56e0\u7ec4\u7684fasta\u6587\u4ef6\u6539\u540d\u4e3agenome.fasta\u5e76\u653e\u5230PRE\/REFRENCE_NAME\/\u6587\u4ef6\u5939\u4e0b\u3002\u4f7f\u7528Fasta2Fastb\u6765\u5c06fasta\u6587\u4ef6\u8f6c\u6362\u4e3a\u5176\u4e8c\u8fdb\u5236\u6587\u4ef6\uff0c\u5728PRE\/REFRENCE_NAME\/\u76ee\u5f55\u4e0b\u751f\u6210genome.fastb\u6587\u4ef6\u3002<\/p>\n<pre>$ Fasta2Fastb IN=PRE\/REFRENCE_NAME\/genome.fasta<\/pre>\n<h2>4. ALLPATHS Cache\u7684\u4f7f\u7528<\/h2>\n<p>PrepareAllPathsInputs.pl\u811a\u672c\u5b9e\u9645\u4e0a\u662f\u5305\u542b\u4e24\u4e2a\u6b65\u9aa4\uff1a<br \/>\n1. \u5c06\u6d4b\u5e8f\u7684\u539f\u59cb\u6587\u672c\u6570\u636e(fastq\u7b49\u6587\u4ef6)\u8f6c\u6362\u6210\u4e8c\u8fdb\u5236\u6570\u636e(fastb\uff0cqualb\u6587\u4ef6)\uff0c\u5e76\u5c06\u5404\u4e2agroup\u6d4b\u5e8f\u6570\u636e\u7684\u4e8c\u8fdb\u5236\u6570\u636e\u653e\u7f6e\u5230\u7f13\u5b58\u6587\u4ef6\u5939\uff1a&lt;DATA&gt;\/read_cache\u3002<br \/>\n2. \u5c06\u90e8\u5206\u6216\u8005\u5168\u90e8\u7684\u4e8c\u8fdb\u5236\u6570\u636e\u7ed3\u5408\u5e76\u751f\u6210\u6240\u9700\u8981\u7684\u8fd0\u7528\u4e8e\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7684\u6570\u636e\u6587\u4ef6\u3002\u56e0\u6b64\uff0c\u4f7f\u7528ALLPATHS Cache\u7684\u4f18\u70b9\uff1aa. \u5f53\u52a0\u5165\u65b0\u7684\u6d4b\u5e8f\u6570\u636e\u6216\u8fdb\u884c\u4e0d\u540c\u6570\u636e\u91cf\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8bc4\u4f30\u65f6\uff0c\u9700\u8981\u518d\u6b21\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u8fd9\u65f6\u53ef\u4ee5\u4ec5\u4ec5\u53ea\u8f6c\u6362\u65b0\u7684\u6d4b\u5e8f\u6570\u636e\uff0c\u8282\u7ea6\u4e86\u91cd\u65b0\u8fdb\u884c\u6570\u636e\u8f6c\u6362\u7684\u65f6\u95f4\u3002\u53ea\u9700\u8981\u5c06\u4e8c\u8fdb\u5236\u6570\u636e\u6839\u636e\u9700\u8981\u6765\u751f\u6210ALLPATHS-LG\u63a5\u53d7\u7684\u6587\u4ef6; b. \u5f53\u6d4b\u5e8f\u6570\u636e\u7684\u6d4b\u5e8f\u8d28\u91cf\u6709phred64\u548cphred33\u517c\u6709\u7684\u65f6\u5019\uff0c\u5219\u9700\u8981\u4f7f\u7528Cache\u6765\u5206\u522b\u8f6c\u6362\u6570\u636e\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">(1)<\/span><span style=\"color: #ff00ff;\">.<\/span><span style=\"color: #ff00ff;\"> \u4f7f\u7528CacheLibs.pl\u5c06\u6587\u5e93\u4fe1\u606f\u8bfb\u5165\u5230Cache<\/span><\/p>\n<p>\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n<pre>CacheLibs.pl\\\r\n  CACHE_DIR=&lt;CACHE_DIR&gt;\\\r\n  IN_LIBS_CSV=in_libs.csv\\\r\n  ACTION=Add<\/pre>\n<p>\u4f7f\u7528\u53c2\u6570\uff1a<\/p>\n<pre><span style=\"color: #ff00ff;\">CACHE_DIR<\/span>\r\n    \u7f13\u5b58\u6587\u4ef6\u5939\u7684\u7edd\u5bf9\u8def\u5f84\u540d\r\n<span style=\"color: #ff00ff;\">IN_LIBS_CSV<\/span>\r\n    \u8f93\u5165\u7684in_libs.csv\u6587\u4ef6\u540d\r\n<span style=\"color: #ff00ff;\">ACTION \u00a0deault: List<\/span>\r\n    Add,List \u6216\u8005 Remove,\u4eceCache\u4e2d\u6dfb\u52a0\uff0c\u5217\u51fa\u6216\u79fb\u9664\u6587\u5e93\u4fe1\u606f\u3002<\/pre>\n<p><span style=\"color: #ff00ff;\">(2)<\/span><span style=\"color: #ff00ff;\">.<\/span><strong><span style=\"color: #ff00ff;\"> \u4f7f\u7528CacheGroups.pl\u5c06\u6587\u672c\u6570\u636e\u6587\u4ef6\u8f6c\u6362\u6210\u4e8c\u8fdb\u5236\u6570\u636e\u6587\u4ef6\u5230Cache<\/span><\/strong><\/p>\n<p>\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n<pre>CacheGroups.pl\\\r\n  CACHE_DIR=&lt;CACHE_DIR&gt;\\\r\n  PICARD_TOOLS_DIR=\/opt\/picard\/bin\\\r\n  IN_GROUPS_CVS=in_groups.csv\\\r\n  TMP_DIR=\/tmp\\\r\n  HOSTS='2,3.host2,4.host3'\\\r\n  ACTION=Add<\/pre>\n<p>\u4f7f\u7528\u53c2\u6570\uff1a<\/p>\n<pre><span style=\"color: #ff00ff;\">CACHE_DIR<\/span>\r\n    \u7f13\u5b58\u6587\u4ef6\u5939\u7684\u7edd\u5bf9\u8def\u5f84\u540d\r\n<span style=\"color: #ff00ff;\">PICARD_TOOLS_DIR<\/span>\r\n    \u82e5\u8f93\u5165\u6570\u636e\u4e3abam\u683c\u5f0f\uff0c\u5219\u9700\u8981\u7528\u5230Picard\u8f6f\u4ef6\uff0c\u8be5\u53c2\u6570\u4e3aPicard\u7684\u8def\u5f84\r\n<span style=\"color: #ff00ff;\">IN_GROUPS_CSV<\/span>\r\n    \u8f93\u5165\u7684in_groups.csv\u6587\u4ef6\u540d\r\n<span style=\"color: #ff00ff;\">PHRED_64  default: 0<\/span>\r\n    \u8f93\u5165\u7684fastq\u7684\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\uff0cTrue: \u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u4e3aPHRED64; False: \u78b1\u57fa\u8d28\u91cf\r\n\u683c\u5f0f\u4e3aPHRED33.\r\n<span style=\"color: #ff00ff;\">OVERWRITE  default: 0<\/span>\r\n    \u662f\u5426\u8986\u76d6\u5df2\u5b58\u5728\u7684\u6570\u636e\u6587\u4ef6\r\n<span style=\"color: #ff00ff;\">TMP_DIR<\/span>\r\n    \u4e34\u65f6\u6587\u4ef6\u5939\u7684\u8def\u5f84\uff0c\u5982\u679c\u6570\u636e\u91cf\u591f\u5927\uff0c\u5219\u5fc5\u987b\u8981\u591f\u5927\r\n<span style=\"color: #ff00ff;\">INCLUDE_NON_PF_READS default: 1<\/span>\r\n    1:\u5305\u542bnon-PF reads\uff1b0:\u4ec5\u4ec5\u53ea\u5305\u542bPF reads.\r\n<span style=\"color: #ff00ff;\">HOSTS<\/span>\r\n    \u5217\u51fa\u5e73\u884cforking\u7684host\u4e3b\u673a(\u8fd9\u4e9b\u4e3b\u673a\u5fc5\u987b\u8981\u80fd\u65e0\u5bc6\u7801\u76f4\u63a5ssh\u8fde\u4e0a)\u3002\u6bd4\u5982\u201c2,3.\r\nhost2,4.host3\"\u8868\u793a\u4f7f\u7528\u672c\u5730\u673a\u5668\u76842\u4e2aCPU\u7ebf\u7a0b\uff0chost2\u673a\u5668\u76843\u4e2aCPU\u7ebf\u7a0b\u548chost3\u673a\r\n\u5668\u76844\u4e2aCPU\u7ebf\u7a0b\u3002\r\n<span style=\"color: #ff00ff;\">ACTION  default: List<\/span>\r\n    Add,List \u6216\u8005 Remove,\u4eceCache\u4e2d\u6dfb\u52a0\uff0c\u5217\u51fa\u6216\u79fb\u9664group\u7684\u6570\u636e\u4fe1\u606f\u3002<\/pre>\n<p><span style=\"color: #ff00ff;\">(3). \u4f7f\u7528CacheToAllPathsInputs.pl\u6765\u751f\u6210ALLPATHS\u7684\u8f93\u5165\u6570\u636e\u3002<\/span><br \/>\n\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n<pre>CacheToAllPathsInputs.pl\\\r\n  CACHE_DIR=&lt;CACHE_DIR&gt;\\\r\n  DATA_DIR=DATA_DIR\\\r\n  GROUPS=\"{group1,group2}\"\\\r\n  FRAG_FRAC=100%\\\r\n  JUMP_FRAC=100%<\/pre>\n<p>\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre><span style=\"color: #ff00ff;\">CACHE_DIR<\/span>\r\n    \u7f13\u5b58\u6587\u4ef6\u5939\u7684\u7edd\u5bf9\u8def\u5f84\u540d\r\n<span style=\"color: #ff00ff;\">DATA_DIR<\/span>\r\n    DATA\u6587\u4ef6\u5939\u5c31\u7edd\u5bf9\u8def\u5f84\u540d\r\n<span style=\"color: #ff00ff;\">GROUPS<\/span>\r\n    \u9700\u8981\u8f6c\u6362\u7684\u5230ALLPATHS\u7684\u8f93\u5165\u6570\u636e\u7684groups\u540d\u3002\u683c\u5f0f\u4e3a\"{group1,group2,group\r\n...}\"\r\n<span style=\"color: #ff00ff;\">IN_GROUPS_CSV<\/span>\r\n    in_groups.csv\u6587\u4ef6\u540d\uff0c\u548c GROUPS \u53c2\u6570\u4e8c\u9009\u4e00\r\n<span style=\"color: #ff00ff;\">FRAG_FRAC<\/span>\r\n    \u4f7f\u7528\u5c0f\u7247\u6bb5\u5e93reads\u7684\u6bd4\u4f8b\u3002\u6bd4\u5982 30% \u6216 0.3 \u3002\u5982\u679c\u8bbe\u5b9a\u4e86\u6b64\u503c\uff0c\u5219\u4e0d\u80fd\u540c\u65f6\u8bbe\u5b9a\r\nFRAG_COVERAGE\u3002\r\n<span style=\"color: #ff00ff;\">JUMP_FRAC<\/span>\r\n    \u4f7f\u7528\u5927\u7247\u6bb5\u5e93reads\u7684\u6bd4\u4f8b\u3002\u6bd4\u5982 20% \u6216 0.2 \u3002\u5982\u679c\u8bbe\u5b9a\u4e86\u6b64\u503c\uff0c\u5219\u4e0d\u80fd\u540c\u65f6\u8bbe\u5b9a\r\nJUMP_COVERAGE\u3002\r\n<span style=\"color: #ff00ff;\">LONG_JUMP_FRAC<\/span>\r\n    \u4f7f\u7528\u8d85\u5927\u7247\u6bb5\u5e93reads\u7684\u6bd4\u4f8b\u3002 \u6bd4\u5982 90% \u6216 0.9 \u3002\u5982\u679c\u8bbe\u5b9a\u4e86\u6b64\u503c\uff0c\u5219\u4e0d\u80fd\u540c\u65f6\r\n\u8bbe\u5b9aLONG_JUMP_COVERAGE\u3002\r\n<span style=\"color: #ff00ff;\">FRACTIONS<\/span>\r\n    \u540c\u65f6\u8bbe\u7f6e\u4e0a\u8ff03\u4e2a\u53c2\u6570\u3002\u6bd4\u5982\"{0.5,30%,100%}\"\r\n<span style=\"color: #ff00ff;\">GENOME_SIZE<\/span>\r\n    \u4f30\u8ba1\u7684\u57fa\u56e0\u7ec4\u5927\u5c0f\uff0c\u7528\u6765\u8ba1\u7b97\u5bf9\u5e94\u8986\u76d6\u5ea6\u6240\u5bf9\u5e94\u7684reads\u6570\r\n<span style=\"color: #ff00ff;\">FRAG_COVERAGE<\/span>\r\n    \u6240\u671f\u671b\u7684\u5c0f\u7247\u5ea6\u5e93\u7684\u8986\u76d6\u5ea6\uff0c\u6bd4\u5982 45. \u8981\u6c42GENOME_SIZE\u6709\u8bbe\u5b9a\r\n<span style=\"color: #ff00ff;\">JUMP_COVERAGE<\/span>\r\n    \u6240\u671f\u671b\u7684\u5927\u7247\u5ea6\u5e93\u7684\u8986\u76d6\u5ea6\uff0c\u6bd4\u5982 45. \u8981\u6c42GENOME_SIZE\u6709\u8bbe\u5b9a\r\n<span style=\"color: #ff00ff;\">LONG_JUMP_COVERAGE<\/span>\r\n    \u6240\u671f\u671b\u7684\u8d85\u5927\u7247\u5ea6\u5e93\u7684\u8986\u76d6\u5ea6\uff0c\u6bd4\u5982 1. \u8981\u6c42GENOME_SIZE\u6709\u8bbe\u5b9a\r\n<span style=\"color: #ff00ff;\">COVERAGES<\/span>\r\n    \u540c\u65f6\u8bbe\u7f6e\u4e0a\u8ff03\u4e2a\u53c2\u6570\uff0c\u6bd4\u5982\"{45,50,2}\"\r\n<span style=\"color: #ff00ff;\">LONG_READ_MIN_LEN  default: 500<\/span>\r\n    \u8bbe\u7f6e\u88ab\u79f0\u4e3along unpaired read\u7684\u9608\u503c(\u9002\u7528\u4e8ePacBio reads)\r\n<span style=\"color: #ff00ff;\">PLOIDY \u00a0<\/span>\r\n    \u751f\u6210ploidy\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u5c31\u5305\u542b\u4e00\u4e2a\u6570\u5b57 1 \u6216\u8005 2 \u30021\u8868\u793a\u57fa\u56e0\u7ec4\u4e3a\u5355\u500d\u4f53\u578b\uff0c2\u8868\r\n\u793a\u53cc\u500d\u4f53\u578b\u3002\u5982\u679c\u6ca1\u6709\u8be5\u53c2\u6570\uff0c\u5219\u4e0d\u751f\u6210ploidy\u6587\u4ef6<\/pre>\n<h1>\u56db. \u601d\u8003\u9898<\/h1>\n<p>\u5bf9\u4e00\u4e2a\u7b80\u5355\u7684\u771f\u83cc\u7269\u79cd\uff0c\u8fd0\u7528Illumina Hiseq2000\u5e73\u53f0\uff0c\u6784\u5efa\u4e86180bp,500bp,3000bp\u957f\u5ea6\u76843\u4e2aDNA\u7247\u6bb5\u6587\u5e93\uff0c\u5206\u522b\u8fdb\u884c\u4e86\u6d4b\u5e8f\u3002\u83b7\u5f97\u4e86\u76f8\u5e94\u7684fastq\u6570\u636e\u6587\u4ef6\uff0c\u5982\u4f55\u4f7f\u7528ALLPATHS-LG\u6765\u8fdb\u884c\u57fa\u56e0\u7ec4\u7684<em>De novo<\/em>\u7ec4\u88c5\uff1f<\/p>\n<h2>1. <a href=\"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=665\" target=\"_blank\">\u5b89\u88c5ALLPATHS-LG\u5230Unix\u7cfb\u7edf\u670d\u52a1\u5668\u4e0a<\/a><\/h2>\n<h2>2. \u51c6\u5907\u6d4b\u5e8f\u7684\u6570\u636e\u6587\u4ef6<\/h2>\n<p>\u6d4b\u5e8f\u7684\u6570\u636e\u6587\u4ef6\u5982\u4e0b\uff0c\u5e76\u653e\u7f6e\u5230\u5f53\u524d\u5de5\u4f5c\u76ee\u5f55\u4e0b\u7684 seq \u6587\u4ef6\u5939\u4e2d\u3002<\/p>\n<pre>180.reads1.fastq    180.reads2.fastq\r\n500.reads1.fastq    500.reads2.fastq\r\n3000.reads1.fastq   3000.reads2.fastq<\/pre>\n<h2>3. in_libs.csv \u548c in_groups.csv \u6587\u4ef6\u7684\u51c6\u5907<br \/>\n\u4e24\u4e2a\u6587\u4ef6\u90fd\u653e\u7f6e\u5230\u5f53\u524d\u5de5\u4f5c\u76ee\u5f55\u4e0b\u3002 in_libs.csv \u5185\u5bb9\u5982\u4e0b\uff1a<\/h2>\n<pre>library_name, project_name, organism_name, type, paired, frag_size, frag_stddev, insert_size, insert_stddev, read_orientation, genomic_start, genomic_end\r\nIllumina_180bp, species, species.genome, fragment, 1, 180, 20, , , inward, 0, 0\r\nIllumina_500bp, species, species.genome, fragment, 1, 500, 50, , , inward, 0, 0\r\nIllumina_3000bp, species, species.genome, jumping, 1, , , 3000, 500, outward, 0, 0<\/pre>\n<p>in_groups.csv \u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n<pre>group_name, library_name, file_name\r\n180, Illumina_180bp, .\/seq\/180.reads?.fastq\r\n500, Illumina_500bp, .\/seq\/500.reads?.fastq\r\n3000, Illumina_3000bp, .\/seq\/3000.reads?.fastq<\/pre>\n<h2>4. \u4f7f\u7528PrepareAllPathsInputs.pl\u6765\u5bf9\u6570\u636e\u8fdb\u884c\u8f6c\u6362<\/h2>\n<p>\u5c06\u4ee5\u4e0b\u5185\u5bb9\u5199\u5165prepare.sh\u5e76\u8fd0\u884c<\/p>\n<pre>#!\/bin\/sh\r\nulimit -s 100000\r\nmkdir -p species.genome\/data\r\nPrepareAllPathsInputs.pl\\\r\n DATA_DIR=$PWD\/species.genome\/data\\\r\n PLOIDY=1\\\r\n IN_GROUPS_CSV=in_groups.csv\\\r\n IN_LIBS_CSV=in_libs.csv\\\r\n OVERWRITE=True\\\r\n | tee prepare.out<\/pre>\n<h2>5. \u8fd0\u884cALLPATHS-LG\u4e3b\u7a0b\u5e8f\u8fdb\u884c\u57fa\u56e0\u7ec4\u7684<em>De novo<\/em>\u7ec4\u88c5<\/h2>\n<p>\u5c06\u4ee5\u4e0b\u5185\u5bb9\u5199\u5165\u5230assemble.sh\u4e2d\uff0c\u5e76\u8fd0\u884c<\/p>\n<pre>#!\/bin\/sh\r\nulimit -s 100000\r\nRunAllPathsLG\\\r\n PRE=$PWD\\\r\n REFERENCE_NAME=species.genome\\\r\n DATA_SUBDIR=data\\\r\n RUN=run\\\r\n SUBDIR=test\\\r\n OVERWRITE=True\\\r\n MAXPAR=8\\\r\n | tee -a assemble.out<\/pre>\n<h2>6. \u7ed3\u679c\u6587\u4ef6<\/h2>\n<p>\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\u6587\u4ef6\u4f4d\u4e8e.\/species.genome\/data\/run\/ASSEMBLIES\/test\/final.assembly.fasta\u6587\u4ef6\u3002\u540c\u4e00\u4e2a\u76ee\u5f55\u4e0b\u6709\u4e00\u4e2a\u6587\u4ef6final.assembly.efasta\u4e5f\u662f\u7ec4\u88c5\u7ed3\u679c\u3002<br \/>\nefasta\u683c\u5f0f\u5373\u201cenhanced fasta\u201d\u3002<br \/>\nefasta\u548cfasta\u7684\u533a\u522b\uff1a<\/p>\n<pre>fasta: ATGTCNTGTCG\r\nefasta:ATGTC{A,T}GTCG<\/pre>\n<p>efasta\u4f7f\u7ed3\u679c\u66f4\u660e\u786e\uff0c\u4f46\u662f\u5728\u6570\u636e\u5904\u7406\u7684\u65f6\u5019\uff0c\u4e0d\u6613\u517c\u5bb9\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4e00\u3001ALLPATH\u7b80\u4ecb ALLPATHS-LG\u662f\u4e00\u4e2a\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\uff0c\u9002\u5408\u4e8e\u7ec4\u88c5s &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=719\">\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":[33,39,40],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/719"}],"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=719"}],"version-history":[{"count":51,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/719\/revisions"}],"predecessor-version":[{"id":1622,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/719\/revisions\/1622"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=719"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=719"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=719"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}