{"id":2135,"date":"2014-06-10T02:59:19","date_gmt":"2014-06-09T18:59:19","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2135"},"modified":"2014-06-10T13:58:08","modified_gmt":"2014-06-10T05:58:08","slug":"%e4%bd%bf%e7%94%a8-cisa-%e8%bf%9b%e8%a1%8c%e5%a4%9a%e4%b8%aa-genome-assemblies-%e7%9a%84%e6%95%b4%e5%90%88","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2135","title":{"rendered":"\u4f7f\u7528 CISA \u8fdb\u884c\u591a\u4e2a genome Assemblies \u7684\u6574\u5408"},"content":{"rendered":"

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

CISA (Contig Integrator for Sequence Assembly). \u4e3b\u8981\u7528\u4e8e\u7ec6\u83cc\u57fa\u56e0\u7ec4\uff08\u5c0f\u57fa\u56e0\u7ec4\uff09\u7684\u6574\u5408\u3002\u8be5\u8f6f\u4ef6\u4f7f\u7528\u7b80\u5355\uff0c\u7b97\u6cd5\u8f83\u597d\u3002
\nCISA \u8f6f\u4ef6\u5b98\u7f51\uff1ahttp:\/\/sb.nhri.org.tw\/CISA\/en\/CISA<\/a>
\nCISA\u53c2\u8003\u6587\u732e\uff1aLin S H, Liao Y C. CISA: contig integrator for sequence assembly of bacterial genomes[J]. PloS one, 2013, 8(3): e60843.<\/a><\/p>\n

2. CISA \u7b97\u6cd5<\/h1>\n

CISA\u52064\u6b65\u8fdb\u884c\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff1a
\n\"CISA\u7b97\u6cd5\u56fe\"<\/p>\n

2.1 \u9274\u5b9a\u4ee3\u8868\u6027\u7684 contigs \u5e76\u5bf9\u5176\u8fdb\u884c\u5ef6\u4f38<\/h1>\n

\u9996\u5148\uff0c\u5c06\u6240\u6709 Assemblies \u7684 contigs \u8fdb\u884c\u5408\u5e76\uff0c\u5e76\u6309\u957f\u5ea6\u8fdb\u884c\u6392\u5e8f\u3002\u7136\u540e\u8c03\u7528 NUCmer \u8f6f\u4ef6\u6309\u4ece\u957f\u5230\u77ed\u7684\u987a\u5e8f\u5bf9\u5e8f\u5217\u9010\u4e2a\u8fdb\u884c\u57fa\u56e0\u7ec4\u6bd4\u5bf9\u3002\u901a\u8fc7\u6b64\u65b9\u6cd5\u6765\u5f97\u5230\u5e8f\u5217\u5728\u5404\u4e2a Assemblies \u4e4b\u95f4\u7684\u91cd\u53e0\u72b6\u51b5\uff0c\u5e76\u5c06\u7ed3\u679c\u5199\u5165\u5230 CISA1\/explained.txt(\u5e8f\u5217\u91cd\u53e0\u4fe1\u606f) \u548c CISA1\/Extend_info(\u5e8f\u5217\u5ef6\u4f38\u4fe1\u606f) \u6587\u4ef6\u4e2d\u3002
\n\u8bbe\u5b9a\u7684\u9608\u503c\u4e3a\uff1a\u975e\u4ee3\u8868\u6027\u5e8f\u5217\u4e0e\u4ee3\u8868\u6027\u5e8f\u5217\u7684\u6bd4\u5bf9\u7ed3\u679c\u8fbe\u5230 >95% \u8986\u76d6\u5ea6 \u548c >95% \u7684\u4e00\u81f4\u6027\uff1b \u6216\u975e\u4ee3\u8868\u6027\u5e8f\u5217\u8d85\u51fa\u4e86\u4ee3\u8868\u6027\u5e8f\u5217\u7684\u4e24\u7aef\u65f6\uff0c\u6bd4\u5bf9\u7ed3\u679c >80% \u8986\u76d6\u5ea6 \u548c >95% \u7684\u4e00\u81f4\u6027\u3002
\n\u901a\u8fc7\u8fd9\u79cd\u65b9\u6cd5\uff0c\u6700\u7ec8\u5f97\u5230\u5ef6\u957f\u7684\u4ee3\u8868\u6027\u5e8f\u5217\uff0c\u8f93\u51fa\u5230 R1_Contigs.fa \u6587\u4ef6\u4e2d\u3002
\n\u5982\u56fe\u6240\u793a\uff1a\u5bf9 3 \u4e2a Assemblies \u8fdb\u884c CISA \u5206\u6790\u3002\u9996\u5148\u627e\u5230\u6240\u6709 contigs \u5e8f\u5217\u4e2d\u6700\u957f\u7684 contig \u5e8f\u5217\uff08\u84dd\u8272\u7ebf\u6761\u8868\u793a\uff09\u8fdb\u884c\u5168\u57fa\u56e0\u7ec4\u6bd4\u5bf9\uff0c\u5f97\u5230\u4e86\u7b2c 1 \u8f6e\u7ed3\u679c\uff1b\u7136\u540e\u4f7f\u7528\u5269\u4e0b\u7684\u5e8f\u5217\uff08+\u53f7\u540e\u9762\u7684\u5e8f\u5217\uff09\u6311\u51fa\u6700\u957f\u7684 contig \u5e8f\u5217\uff08\u84dd\u8272\u7ebf\u6761\u8868\u793a\uff09\uff0c\u5bf9\u5269\u4e0b\u7684\u5e8f\u5217\u4f7f\u7528 NUCmer \u8fdb\u884c\u6bd4\u5bf9\uff0c\u5f97\u5230\u7b2c 2 \u8f6e\u7ed3\u679c\uff1b \u7ee7\u7eed\u4f7f\u7528\u5269\u4e0b\u7684\u5e8f\u5217\u6311\u51fa\u6700\u957f\u7684 contig \u5e8f\u5217\uff08\u9ed1\u8272\u7ebf\u6761\u8868\u793a\uff09\uff0c\u6700\u4e3a\u4ee3\u8868\u6027\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\uff1b\u6700\u7ec8\u5f97\u5230\u4e86 4 \u6761\uff08\u84dd\u84dd\u9ed1\u7ea2\uff09\u4ee3\u8868\u6027\u5e8f\u5217\uff0c\u5176\u4e2d\u7684\u7a7a\u5fc3\u692d\u5706\u548c\u5b9e\u5fc3\u7bad\u5934\u5206\u522b\u4ee3\u8868\u5ef6\u4f38\u7684\u4f4d\u7f6e\u548c\u65b9\u5411\u3002<\/p>\n

2.2 \u5bf9 misassembled \u7684 contigs \u8fdb\u884c\u53bb\u9664\u6216\u622a\u65ad, \u5e76\u5bf9 contigs\u4e24\u7aef\u4e0d\u786e\u5b9a\u533a\u57df\u8fdb\u884c\u622a\u77ed<\/h2>\n

\u5c06 R1_Contigs.fa \u7684\u5e8f\u5217\u4f7f\u7528 NUCmer \u6bd4\u5bf9\u5230\u6240\u6709\u7684 contigs \u4e0a\u3002\u901a\u8fc7\u6bd4\u5bf9\u7ed3\u679c\uff0c\u4ece\u800c\u5bf9 misassembled \u7684 contigs \u8fdb\u884c\u53bb\u9664\u6216\u622a\u65ad, \u6216\u5bf9 contigs\u4e24\u7aef\u4e0d\u786e\u5b9a\u533a\u57df\u8fdb\u884c\u622a\u77ed\u3002
\n\u5982\u56fe\u6240\u793a\uff1a
\nPhase(2)\u5de6\u56fe\u8868\u793a 1 \u6761\u4ee3\u8868\u6027\u5e8f\u5217\u6bd4\u5bf9\u5230\u4e86 2 \u4e2a\u4e0d\u540c\u7684 contigs \u7684\u4e2d\u95f4\uff0c\u5219\u8868\u660e\u8be5\u4ee3\u8868\u6027\u5e8f\u5217\u662f\u9519\u8bef\u7684\u7ec4\u88c5\uff0c\u5219\u53bb\u9664\u8be5\u4ee3\u8868\u6027\u5e8f\u5217\uff0c\u540c\u65f6\u5f15\u8fdb\u76f8\u5e94\u7684\u80fd\u6bd4\u5bf9\u5230\u8be5\u4ee3\u8868\u6027\u5e8f\u5217\u7684 contigs\u3002\u8fd9\u4e9b\u4fe1\u606f\u5728 CISA2\/Remove_Info \u6587\u4ef6\u4e2d\u3002
\nPhase(2)\u53f3\u56fe\u8868\u793a 1 \u6761\u4ee3\u8868\u6027\u5e8f\u5217\u4e2d\u95f4\u533a\u57df\u6ca1\u6709\u5bf9\u5e94\u7684 contigs \u80fd\u5339\u914d\uff0c\u5219\u8868\u660e\u8be5\u5e8f\u5217\u662f\u9519\u8bef\u7684\u7ec4\u88c5\uff0c\u5219\u5c06\u8be5\u533a\u57df\u8fdb\u884c\u53bb\u9664\uff0c\u622a\u65ad\u8be5\u4ee3\u8868\u6027\u5e8f\u5217\u3002\u6709\u5173Gaps \u7684\u4fe1\u606f\u5728 CISA2\/Gaps \u6587\u4ef6\u4e2d\uff0c\u82e5 Gap \u957f\u5ea6\u5927\u4e8e\u5176\u4ee3\u8868\u6027\u5e8f\u5217\u957f\u5ea6\u7684 95%\uff0c\u5219\u53bb\u9664\u8be5\u5e8f\u5217\u3002
\n\u6b64\u5916\uff0c\u5bf9\u4ee3\u8868\u6027\u5e8f\u5217\u9996\u5c3e\u4e0d\u786e\u5b9a\u6027\u533a\u57df\u7684\u4fe1\u606f\u5728 CISA2\/clip_info \u548c CISA2\/clip_out \u6587\u4ef6\u4e2d\u3002
\n\u6700\u7ec8\uff0c\u5bf9 misassembled \u7684 contigs \u8fdb\u884c\u5904\u7406\u540e\uff0c\u5f97\u5230\u7ed3\u679c\u6587\u4ef6 R2_Contigs.fa\u3002\u8be5\u6587\u4ef6\u7684\u5e8f\u5217\u603b\u957f\u5ea6\u504f\u5927\u3002<\/p>\n

2.3 \u901a\u8fc7 Overlap \u4fe1\u606f\u5c06 contigs \u878d\u5408<\/h2>\n

\u5982\u679c 2 \u4e2a contigs \u6709 end-to-end \u91cd\u53e0\uff0c\u5e76\u4e14\u91cd\u53e0\u533a\u5bf9\u8f83\u5c0f contigs \u957f\u5ea6\u7684\u6bd4\u4f8b >30%, \u5219\u5c06\u5176\u8fdb\u884c\u878d\u5408\u3002\u4f7f\u7528\u591a\u8f6e blastn \u8fdb\u884c\u8fed\u4ee3\u6765\u878d\u5408 contigs \u5e8f\u5217\u3002\u540c\u65f6\u4e5f\u8fdb\u884c\u91cd\u590d\u5e8f\u5217\u9274\u5b9a\u3002
\n\u878d\u5408\u4fe1\u606f\u5199\u5165\u5230\u6bcf\u8f6e\u6587\u4ef6\u5939\u4e0b\u7684 Extend_info \u6587\u4ef6\u4e2d\uff0c\u540c\u65f6\u6bcf\u8f6e\u751f\u6210 temp.fa \u6587\u4ef6\uff0c\u4f5c\u4e3a\u4e0b\u4e00\u8f6e blastn \u7684\u6570\u636e\u5e93\u6784\u5efa\u7684\u8f93\u5165\u6587\u4ef6\u3002
\n\u91cd\u590d\u5e8f\u5217\u4fe1\u606f\u6587\u4ef6\u5199\u5165\u5230\u6bcf\u8f6e\u6587\u4ef6\u5939\u4e0b\u7684 Repeat_Region.txt \u6587\u4ef6\u4e2d\u3002<\/p>\n

2.4 \u901a\u8fc7 small overlap \u8fdb\u884c contigs \u878d\u5408<\/h2>\n

\u4e0a\u4e00\u6b65\u9aa4\u5c06 contigs \u8fdb\u884c\u878d\u5408\u9700\u8981 >30% \u8986\u76d6\u5ea6\u7684 overlap\uff0c\u540c\u65f6\u4e5f\u9274\u5b9a\u4e86\u91cd\u590d\u5e8f\u5217\u3002\u5982\u56fe\u6240\u793a\uff1aPhase3\u4e2d\uff0c\u9ed1\u8272\u4e0e\u7ea2\u8272\u7ebf\u6761\u91cd\u53e0\u533a\u6bd4\u4f8b\u5927\uff0c\u88ab\u6574\u5408\u5230\u4e00\u8d77\uff0c\u8be5\u5e8f\u5217\u548c\u5176\u4ed6\u4e24\u6761\u84dd\u8272\u5e8f\u5217\u7684overlap\u6bd4\u8f83small\uff0c\u4e0d\u80fd\u8fdb\u884c\u878d\u5408\u3002\u4f46\u662f\u9274\u5b9a\u4e86\u5176\u91cd\u590d\u5e8f\u5217\uff08\u7eff\u8272\u5757\u8868\u793a\uff09\u540e\uff0c\u901a\u8fc7\u672c\u6b65\u9aa4\uff0c\u82e5\u91cd\u590d\u533a\u57df\u957f\u5ea6\u5c0f\u4e8e\u5176 small overlap\uff0c\u5219\u80fd\u5c06 contigs \u8fdb\u884c\u878d\u5408\u3002
\n\u6b64\u6b65\u9aa4\u548c\u4e0a\u4e00\u6b65\u9aa4\u7c7b\u4f3c\uff0c\u4f7f\u7528 blastn \u8fdb\u884c\u591a\u8f6e\u8fd0\u7b97\u3002\u540c\u65f6\u5c06\u7ed3\u679c\u5199\u5165\u5230\u6bcf\u8f6e\u6587\u4ef6\u5939\u7684 Extend_info \u548c temp.fa \u6587\u4ef6\u4e2d\u3002
\n\u6700\u7ec8\u7684\u8f93\u51fa\u6587\u4ef6\u4e3a CISA.fa (\u7531 cisa.config \u914d\u7f6e\u6587\u4ef6\u6307\u5b9a\u7684\u540d\u79f0)<\/p>\n

3. CISA \u7684\u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h1>\n
\r\n$ wget http:\/\/sb.nhri.org.tw\/CISA\/upload\/en\/2014\/3\/CISA_20140304-05194132.tar\r\n$ tar xf CISA_20140304-05194132.tar -C \/opt\/biosoft\r\n<\/pre>\n
4. CISA \u7684\u4f7f\u7528<\/h1>\n
4.1 \u521b\u5efa merge.config \u914d\u7f6e\u6587\u4ef6<\/h2>\n
\u914d\u7f6e\u6587\u4ef6\u5982\u4e0b\uff1a<\/p>\n
\r\ncount=3 \r\ndata=abyss.fasta,title=abyss  \r\ndata=velvet.fasta,title=velvet\r\ndata=allpathslg.fasta,title=allpathslg\r\nMaster_file=merge_contigs.fa\r\nmin_length=100 (default:100)\r\nGap=11\r\n<\/pre>\n
4.2 Merge.py<\/h2>\n
\r\n$ \/opt\/biosoft\/CISA1.3\/Merge.py merge.config\r\n<\/pre>\n
\u6839\u636e\u4e0a\u9762 merge.config \u914d\u7f6e\u6587\u4ef6\u4fe1\u606f\uff0c\u5bf9 3 \u4e2a Assemblies \u7684 contigs \u5e8f\u5217\u8fdb\u884c\u63d0\u53d6\uff0c\u5e76\u6574\u5408\u5230 merge_contigs.fasta \u6587\u4ef6\u4e2d\uff0c\u540c\u65f6\u8f93\u51fa\u5404\u4e2a Assemblies \u7684 contigs size\u3002<\/p>\n
4.3 \u521b\u5efa cisa.config \u914d\u7f6e\u6587\u4ef6<\/h2>\n
\u914d\u7f6e\u6587\u4ef6\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n
\r\ngenome=47814562 (\u586b\u5199Assemblies\u4e2d\u6700\u5927\u7684 contigs size)\r\ninfile=merge_contigs.fa\r\noutfile=cisa.contig.fa\r\nnucmer=\/opt\/biosoft\/MUMmer3.23\/nucmer\r\nR2_Gap=0.95 (default:0.95)\r\nCISA=\/opt\/biosoft\/CISA1.3\r\nmakeblastdb=\/opt\/biosoft\/ncbi-blast\/bin\/makeblastdb\r\nblastn=\/opt\/biosoft\/ncbi-blast\/bin\/blastn\r\n<\/pre>\n
4.4 CISA.py<\/h2>\n
\r\n$ \/opt\/biosoft\/CISA1.3\/CISA.py cisa.config\r\n<\/pre>\n
\u542f\u52a8\u4e3b\u7a0b\u5e8f\u8fdb\u884c\u8fd0\u7b97\u3002\u57fa\u56e0\u7ec4\u8d8a\u5927\uff0cAssemblies \u6570\u76ee\u8d8a\u591a\uff0c\u8017\u65f6\u8d8a\u591a\uff08\u5448\u51e0\u4f55\u7ea7\u6570\u589e\u52a0\uff09\u3002<\/p>\n
5. \u601d\u8003<\/h1>\n
CISA \u5e94\u8be5\u8981\u4fee\u6539\u4e0b\uff0c\u5728\u7b2c 2 \u6b65\u8fdb\u884c\u5e76\u884c\u5316\u8fd0\u7b97\uff0c\u4ee5\u63d0\u9ad8\u901f\u5ea6\u3002
\n\u53ef\u4ee5\u5206\u6279\u8fdb\u884c\u4e24\u4e24\u878d\u5408\uff0c\u76f4\u5230\u6700\u7ec8\u878d\u5408\u3002\u591a\u4e2a\u4e24\u4e24\u878d\u5408\u8fdb\u884c\u5e76\u884c\u5316\u8fd0\u7b97\u3002
\n\u8fdb\u884c\u5927\u57fa\u56e0\u7ec4\u7684\u878d\u5408\u65f6\uff0cCISA \u4e0d\u9002\u7528\u4e86\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
1. CISA \u7b80\u4ecb CISA (Contig Integrator for S … \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\/2135"}],"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=2135"}],"version-history":[{"count":8,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2135\/revisions"}],"predecessor-version":[{"id":2143,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2135\/revisions\/2143"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2135"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2135"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2135"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}