{"id":2331,"date":"2015-08-25T17:00:07","date_gmt":"2015-08-25T09:00:07","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2331"},"modified":"2015-08-25T17:00:07","modified_gmt":"2015-08-25T09:00:07","slug":"%e4%bd%bf%e7%94%a8abacas%e8%bf%9b%e8%a1%8c%e6%9c%89%e5%8f%82%e8%80%83%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%9a%84contigs%e8%bf%9e%e6%8e%a5","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2331","title":{"rendered":"\u4f7f\u7528ABACAS\u8fdb\u884c\u6709\u53c2\u8003\u57fa\u56e0\u7ec4\u7684contigs\u8fde\u63a5"},"content":{"rendered":"

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

ABACAS \u7528\u4e8e\u5728\u6709\u53c2\u8003\u5e8f\u5217\u7684\u60c5\u51b5\u4e0b\uff0c\u5bf9contigs\u5e8f\u5217\u8fdb\u884c\u8fde\u63a5\u3002\u8f6f\u4ef6\u5b98\u7f51\uff1ahttp:\/\/abacas.sourceforge.net\/<\/a><\/p>\n

2. ABACAS \u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n

ABACAS\u662f\u4e00\u652fperl\u7a0b\u5e8f\uff0c\u5176\u8fd0\u884c\u9700\u8981\u5b89\u88c5\u6709MUMmer\u3002<\/p>\n

\r\n$ wget http:\/\/sourceforge.net\/projects\/abacas\/files\/abacas.1.3.1.pl\r\n$ chmod 755 abacas.1.3.1.pl\r\n$ mv abacas.1.3.1.pl ~\/bin\/\r\n$ ln -s ~\/bin\/abacas.1.3.1.pl ~\/bin\/abacas.pl\r\n$ perl -p -i -e 's#\/usr\/local\/bin\/perl#\/usr\/bin\/perl#' ~\/bin\/abacas.1.3.1.pl\r\n<\/pre>\n
3. ABACAS \u7684\u4f7f\u7528<\/h1>\n
ABACAS \u7684\u7b80\u5355\u4f8b\u5b50\uff1a<\/p>\n
\r\n$ abacas.pl -r ref.fasta -q query.fasta -p nucmer -o out_prefix\r\n<\/pre>\n
ABACAS \u7684\u4f7f\u7528\u53c2\u6570\uff1a<\/p>\n
\r\n-r string\r\n    \u8f93\u5165\u53c2\u8003\u5e8f\u5217\u3002\u53c2\u8003\u5e8f\u5217\u4e3afasta\u683c\u5f0f\u5e76\u4ec5\u67091\u6761\u5e8f\u5217\u3002\r\n-q string\r\n    \u8f93\u5165query\u5e8f\u5217\u3002query\u5e8f\u5217\u4e3afasta\u683c\u5f0f\u3002\r\n-p nucmer|promer\r\n    \u8be5\u53c2\u6570\u53ef\u4ee5\u8bbe\u4e3anucmer\u6216promer\uff0c\u8868\u793a\u4f7f\u7528\u76f8\u5e94\u7684\u7a0b\u5e8f\u8fdb\u884ccontig ordering\u3002\r\n-o string\r\n    \u8bbe\u5b9a\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\u3002\u9ed8\u8ba4\u4e3aquery.fasta_ref.fastq\u3002\r\n-c\r\n    \u53c2\u8003\u5e8f\u5217\u662f\u4e00\u4e2a\u73af\u3002\r\n-m\r\n    \u4f7f\u7528\u8be5\u53c2\u6570\u540e\uff0c\u5219\u5c06\u5b9a\u4f4d\u5e76\u5b9a\u5411\u7684query\u5e8f\u5217\u6309\u987a\u5e8f\u6253\u5370\u5230\u6587\u4ef6 out_prefix.MULTIFASTA.fa \u4e2d\u3002\r\n-b\r\n    \u4f7f\u7528\u8be5\u53c2\u6570\u540e\uff0c\u5219\u5c06\u672a\u80fd\u5b9a\u4f4d\u7684 congtig \u5e8f\u5217\u5185\u5bb9\u6253\u5370\u5230\u6587\u4ef6 ou_prefix.contigsInbin.fas \u4e2d\u3002\r\n-N\r\n    \u4f7f\u7528\u8be5\u53c2\u6570\u540e\uff0c\u5219\u5c06\u7531\u5b9a\u4f4d\u5b9a\u5411\u7684conitg\u5e8f\u5217\u8fde\u63a5\u800c\u6210\u7684pseudomolecule\u7684\u5e8f\u5217\u6253\u5370\u5230\u6587\u4ef6 out_prefix.NoNs.fasta \u4e2d\u3002\u9ed8\u8ba4\u4e0b\uff0c\u8f93\u51fa\u6587\u4ef6 out_prefix.fasta \u4e2d\u7684 pseudomolecule \u5e8f\u5217\u4e2d congtig \u4e4b\u95f4\u7684 gap \u4f7f\u7528 N \u8868\u793a\uff0c\u6709\u91cd\u53e0\u5219\u52a0 100\u4e2aN\uff1b\u8be5\u53c2\u6570\u5219\u662f\u751f\u6210\u989d\u5916\u7684fasta\u6587\u4ef6\uff0c\u5176\u4e2dcontig\u4e4b\u95f4\u5e8f\u5217\u65e0N\u3002\r\n-t\r\n    \u4f7f\u7528\u8be5\u53c2\u6570\u540e\uff0c\u5219\u5bf9 ou_prefix.contigsInbin.fas \u4e2d\u7684\u5e8f\u5217\u8fd0\u884c blastall\uff0c\u989d\u5916\u751f\u6210 blast.out \u6587\u4ef6\u3002\u4f7f\u7528\u8be5\u53c2\u6570\u5219\u5fc5\u987b\u6709 -b \u53c2\u6570\u3002\r\n-g out_prefix\r\n    \u4f7f\u7528\u8be5\u53c2\u6570\u540e\uff0c\u5219\u5c06 pseudomolecule \u7684gap\u90e8\u5206\u5728ref\u4e0a\u7684\u5e8f\u5217\u7b54\u5e94\u5230\u6587\u4ef6 out_prefix.Gaps_onRef \u4e2d\u3002\r\n-P\r\n    \u4f7f\u7528\u8be5\u53c2\u6570\u540e\uff0c\u5219\u8bbe\u8ba1\u7528\u4e8e close gaps \u7684\u5f15\u7269\u3002\u9700\u8981\u5b89\u88c5 prime3_core\uff0c\u4f46\u6211\u4e2a\u4eba\u52a0\u8be5\u53c2\u6570\u8fd0\u884c\u5931\u8d25\u3002\r\n-R\r\n    \u4f7f\u7528\u8be5\u53c2\u6570\uff0c\u5219\u4e0d\u9700\u8981\u8fd0\u884c mumer\uff0c\u9002\u5408\u4e8e\u591a\u6b21\u8fd0\u884c\u7a0b\u5e8f\uff0c\u8282\u7ea6\u65f6\u95f4\u3002\u4f46\u6211\u4e2a\u4eba\u52a0\u8be5\u53c2\u6570\u8fd0\u884c\u5931\u8d25\u3002\r\n-e\r\n    \u4e0d\u8fdb\u884c contig ordering\uff0c\u6709\u5229\u4e8e\u76f4\u63a5\u8fdb\u884c\u5f15\u7269\u8bbe\u8ba1\u3002\r\n-i int\r\n    \u5141\u8bb8\u7684\u6700\u5c0f\u7684identity\u7684\u767e\u5206\u6bd4\u3002\u9ed8\u8ba4\u4e3a 40\u3002\r\n-v int\r\n    \u5141\u8bb8\u7684\u6700\u5c0f\u7684 contig \u8986\u76d6\u7387\u3002\u9ed8\u8ba4\u4e3a 40\u3002\r\n-V 0|1\r\n    contig\u6bd4\u5bf9\u5230ref\u5e8f\u5217\u4e0a\u7684\u4f4d\u7f6e\u7684\u6570\u76ee\u3002\u9ed8\u8ba4\u4e3a1\u3002\u4f7f\u7528 -V 0 \u8868\u793a\u5c06contig\u5e8f\u5217\u968f\u673a\u653e\u52301\u4e2a\u6bd4\u5bf9\u4e0a\u7684\u4f4d\u70b9\u3002\r\n-l int\r\n    \u4e0d\u4f7f\u7528\u4f4e\u4e8e\u6b64\u957f\u5ea6\u7684contig\u5e8f\u5217\u3002\u9ed8\u8ba4\u4e3a 100\u3002 \r\n-d\r\n    ABACAS\u5728\u8c03\u7528MUmer\u7684\u65f6\u5019\uff0c\u9ed8\u8ba4\u4e0b\u4f7f\u7528\u4e86--maxmatch\u53c2\u6570\u6765\u589e\u52a0\u5339\u914d\uff0c\u4f7f\u7528 -d \u53c2\u6570\u5219\u4f1a\u4f7f\u7528MUmer\u7684\u9ed8\u8ba4\u53c2\u6570\uff0c\u5373\u4e0d\u4f1a\u4f7f\u7528--maxmatch\u53c2\u6570\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. ABACAS\u7b80\u4ecb ABACAS \u7528\u4e8e\u5728\u6709\u53c2\u8003\u5e8f\u5217\u7684\u60c5\u51b5\u4e0b\uff0c\u5bf9contigs … \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":[3],"tags":[39,40],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2331"}],"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=2331"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2331\/revisions"}],"predecessor-version":[{"id":2332,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2331\/revisions\/2332"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2331"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2331"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2331"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}