{"id":2327,"date":"2015-08-25T16:57:28","date_gmt":"2015-08-25T08:57:28","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2327"},"modified":"2015-08-25T16:57:28","modified_gmt":"2015-08-25T08:57:28","slug":"%e4%bd%bf%e7%94%a8sopra%e8%bf%9b%e8%a1%8cscaffold%e8%bf%9e%e6%8e%a5","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2327","title":{"rendered":"\u4f7f\u7528SOPRA\u8fdb\u884cscaffold\u8fde\u63a5"},"content":{"rendered":"

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

SOPRA(Statistical Optimization of Paired Read Assembly)\uff0c\u4e3b\u8981\u7528\u4e8e\u5229\u7528\u6210\u5bf9\u7684reads\u4fe1\u606f\u6765\u8fdb\u884cscaffold\u8fde\u63a5\uff0c\u5176\u51c6\u786e\u6027\u975e\u4ea7\u9ad8\u3002\u5176\u53c2\u8003\u6587\u732e\uff1aDayarian, Adel, Todd P. Michael, and Anirvan M. Sengupta. “SOPRA: Scaffolding algorithm for paired reads via statistical optimization.” BMC bioinformatics 11.1 (2010): 345.<\/a><\/p>\n

2. SOPRA\u7684\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n
\r\n$ wget http:\/\/www.physics.rutgers.edu\/~anirvans\/SOPRA\/SOPRA_v1.4.6.zip\r\n$ mkdir \/opt\/biosoft\/SOPRA_v1.4.6\/\r\n$ unzip SOPRA_v1.4.6.zip -d \/opt\/biosoft\/SOPRA_v1.4.6\/\r\n\u5b89\u88c5\u76ee\u5f55\/opt\/biosoft\/SOPRA_v1.4.6\/\u4e0b\u6709SOPRA\u7684manual\u6587\u6863\r\n$ chmod 755 \/opt\/biosoft\/SOPRA_v1.4.6\/source_codes_v1.4.6\/SOPRA_with_prebuilt_contigs\/*.pl\r\n$ perl -p -i -e 's\\s*$\/\\n\/' \/opt\/biosoft\/SOPRA_v1.4.6\/source_codes_v1.4.6\/SOPRA_with_prebuilt_contigs\/*.pl\r\nSOPRA\u7684\u4e3b\u8981\u8fd0\u884c\u7a0b\u5e8f\u5c31\u662f\u8fd94\u652fperl\u7a0b\u5e8f\u3002\r\n<\/pre>\n
3. SOPRA\u7684\u4f7f\u7528\u6d41\u7a0b<\/h1>\n
SOPRA \u53ef\u4ee5\u652f\u6301 Illumina \u548c SOLID \u7684\u4e8c\u4ee3\u6d4b\u5e8f\u6570\u636e\uff0c\u4f46\u6b64\u5904\u4ec5\u8bb2\u89e3\u4f7f\u7528 Illumina \u7684\u6d4b\u5e8f\u6570\u636e\u3002SOPRA \u4e5f\u652f\u6301\u540c\u65f6\u5229\u7528\u591a\u4e2apaired\u6d4b\u5e8f\u6587\u5e93\u7684\u6570\u636e\uff0c\u540c\u65f6\u652f\u6301paired-end\u548cmate-paired\u6570\u636e\u3002<\/p>\n
3.1 \u51c6\u5907\u8f93\u5165\u6570\u636e<\/h2>\n
\u4e0d\u7ba1\u662fpaired-end\u6216mate-paired\u6570\u636e\uff0c\u9996\u5148\u9700\u8981\u5c06\u6570\u636e\u7684\u65b9\u5411\u8f6c\u6362\u4e3aFR\u65b9\u5411\u3002\u5373\u9700\u8981\u5c06mate-paired\u76842\u7aefreads\u90fd\u8fdb\u884c\u53cd\u5411\u4e92\u8865\u3002\u7136\u540e\uff0c\u9700\u8981\u5c06fatstq\u6587\u4ef62\u7aef\u7684reads\u6587\u4ef6\u5408\u5e76\u4e3a\u4e00\u4e2a\u6587\u4ef6\uff0c\u5e76\u8f6c\u6362\u4e3afasta\u6587\u4ef6\u4f5c\u4e3aSOPRA\u7684\u8f93\u5165\u6570\u636e\u3002
\n\u6b64\u5916\uff0cSOPRA\u8fd8\u9700\u8981contig\u5e8f\u5217\u4f5c\u4e3a\u8f93\u5165\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002
\n\u4ee51\u4e2apaired-end\u6570\u636e\u548c1\u4e2amate-paired\u6570\u636e\u4e3a\u4f8b\uff1a<\/p>\n
\r\n\u5148\u5c06 jumping \u6587\u5e93\u7684\u6570\u636e\u8fdb\u884c\u53cd\u5411\u4e92\u8865\r\n$ fastq_rc.pl jump.1.fastq > 11; mv 11 jump.1.fastq\r\n$ fastq_rc.pl jump.2.fastq > 22; mv 22 jump.2.fastq\r\n\r\n\u7136\u540e\uff0c\u5408\u5e76\u4e24\u7aef\u7684reads\u5e8f\u5217\r\n$ \/opt\/biosoft\/velvet_1.2.10\/contrib\/shuffleSequences_fasta\/shuffleSequences_fastq.pl \\\r\n  frag.1.fastq frag.2.fastq frag.fastq\r\n$ \/opt\/biosoft\/velvet_1.2.10\/contrib\/shuffleSequences_fasta\/shuffleSequences_fastq.pl \\\r\n  jump.1.fastq jump.1.fastq jump.fastq\r\n\r\n\u518d\u5c06fastq\u8f6c\u6362\u4e3afasta\r\n$ perl -e '$num = 1; while (<>) { print \">$num\\n\"; $_=<>; print; $_=<>; $_=<>; $num ++; }' frag.fastq > frag.fasta\r\n$ perl -e '$num = 1; while (<>) { print \">$num\\n\"; $_=<>; print; $_=<>; $_=<>; $num ++; }' jump.fastq > jump.fasta\r\n<\/pre>\n
3.2 SOPRA \u5bf9contigs\u5e8f\u5217\u548c\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u683c\u5f0f\u5904\u7406<\/h2>\n
\u4f7f\u7528s_prep_contigAseq_v1.4.6.pl\u7a0b\u5e8f\u5bf9\u57fa\u56e0\u7ec4\u7684contig\u5e8f\u5217\u4ee5\u53caillunia\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u5e8f\u5217\u540d\u7684\u4fee\u6539\uff0c\u4ee5\u5229\u4e8e\u540e\u7eed\u7a0b\u5e8f\u8fd0\u884c\u3002<\/p>\n
\r\n$ \/opt\/biosoft\/SOPRA_v1.4.6\/source_codes_v1.4.6\/SOPRA_with_prebuilt_contigs\/s_prep_contigAseq_v1.4.6.pl \\\r\n  -contig contig.fasta -mate frag.fasta jump.fasta -a SOPRA_OUT\/\r\n\r\n\u7a0b\u5e8f\u53c2\u6570\uff1a\r\n-contig string\r\n    \u8f93\u5165\u57fa\u56e0\u7ec4 contigs \u5e8f\u5217\u3002\r\n-mate string\r\n    \u8f93\u5165 illumina \u6570\u636e\u3002\u5982\u679c\u6709\u591a\u4e2a\u6570\u636e\uff0c\u5219\u591a\u4e2afasta\u6587\u4ef6\u4e4b\u95f4\u4f7f\u7528\u7a7a\u683c\u5206\u5f00\u3002\r\n-a string\r\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u5939\u76ee\u5f55\u3002\r\n<\/pre>\n
\u5728 SOPRA_OUT \u76ee\u5f55\u4e2d\u751f\u6210\u4e86 contigs_sopra.fasta\u3001frag_sopra.fasta \u548c jump_sopra.fasta \u6587\u4ef6\u3002\u67e5\u770b\u8fd93\u4e2a\u6587\u4ef6\u5185\u5bb9\uff0c\u53d1\u73b0\u662f\u5bf9fasta\u6587\u4ef6\u4e2d\u7684\u5e8f\u5217\u540d\u8fdb\u884c\u4e86\u4fee\u6539\u3002<\/p>\n
3.3 \u5c06Illumina\u6570\u636e\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4<\/h2>\n
\u53ef\u4ee5\u5229\u7528bowite,bwa\u7b49\u5e8f\u5217\u6bd4\u5bf9\u8f6f\u4ef6\u5c06Illumina\u6570\u636e\u6309\u5355\u7aef\u5e8f\u5217\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e0a\u3002\u82e5\u4e00\u6761\u5e8f\u5217\u6bd4\u5bf9\u5230\u591a\u4e2a\u4f4d\u7f6e\uff0c\u63a8\u8350\u62a5\u544a\u591a\u4e2a\u7ed3\u679c\u3002\u56e0\u4e3a\u540e\u7eed\u7684s_parse_sam_v1.4.6.pl\u7a0b\u5e8f\u4f1a\u53bb\u9664\u6389\u6bd4\u5bf9\u5230\u591a\u4e2a\u4f4d\u7f6e\u7684reads\u3002\u82e5\u4ec5\u62a5\u544a\u6700\u4f18\u7ed3\u679c\uff0c\u6211\u4e0d\u77e5\u9053\u7a0b\u5e8f\u4f1a\u5982\u4f55\u5904\u7406\u3002\u8981\u662f\u4e0d\u53bb\u9664\u8fd9\u6837\u7684\u6bd4\u5bf9\u7ed3\u679c\uff0c\u53ef\u80fd\u4f1a\u5bf9scaffolding\u7684\u51c6\u786e\u6027\u6709\u5f71\u54cd\u3002\u56e0\u6b64\uff0c\u8fd8\u662f\u8981\u6ce8\u610f\u62a5\u544a\u591a\u4e2a\u6bd4\u5bf9\u7ed3\u679c\uff0c\u7279\u522b\u662fbowtie2\u9ed8\u8ba4\u4e0b\u4ec5\u62a5\u544a\u6700\u4f18\u7ed3\u679c\u3002
\n\u6b64\u5916\uff0c\u53bb\u9664reads\u5c3e\u90e8\u78b1\u57fa\u8d28\u91cf\u4f4e\u7684\u78b1\u57fa\u540e\uff0cillumina reads \u7684\u5339\u914d\u7387\u82e5\u662f\u63d0\u9ad8\u5f88\u591a\uff0c\u5219\u63a8\u8350\u53bb\u9664reads\u5c3e\u90e810~20\u4e2a\u78b1\u57fa\uff0c\u518d\u7528\u4e8e\u6bd4\u5bf9\u3002\u7531\u4e8emate-pair\u6570\u636e\u8fdb\u884c\u4e86\u53cd\u5411\u4e92\u8865\uff0c\u5219\u5176\u539f\u672c\u7684\u5c3e\u90e8\u6210\u4e86\u9996\u90e8\u3002<\/p>\n
\r\n$ cd SOPRA_OUT\/\r\n$ bowtie2-build contigs_sopra.fasta contig\r\n$ bowtie2 -p 20 -x contig -k 10 -f -3 15 -U frag_sopra.fasta -S frag_sopra.sam\r\n$ bowtie2 -p 20 -x contig -k 10 -f -5 15 -U jump_sopra.fasta -S jump_sopra.sam\r\n\r\n\u7a0b\u5e8f\u53c2\u6570\uff1a\r\n-k 10\r\n    \u82e5read\u6bd4\u5bf9\u5230\u591a\u4e2a\u4f4d\u70b9\uff0c\u5219\u6700\u591a\u62a5\u544a 10 \u4e2a\u7ed3\u679c\u3002\r\n-3 15\r\n    \u53bb\u9664read\u5c3e\u90e815bp\u78b1\u57fa\u540e\u518d\u7528\u4e8e\u6bd4\u5bf9\u3002\r\n-5 15\r\n    \u53bb\u9664read\u9996\u90e815bp\u78b1\u57fa\u540e\u518d\u7528\u4e8e\u6bd4\u5bf9\u3002\r\n<\/pre>\n
3.4 \u5bf9SAM\u6587\u4ef6\u8fdb\u884c\u5206\u6790<\/h2>\n
\u4f7f\u7528s_parse_sam_v1.4.6.pl\u5bf9sam\u6587\u4ef6\u8fdb\u884c\u5206\u6790\u5e76\u7b80\u5316\u5176\u4fe1\u606f\u3002<\/p>\n
\r\n$ \/opt\/biosoft\/SOPRA_v1.4.6\/source_codes_v1.4.6\/SOPRA_with_prebuilt_contigs\/s_parse_sam_v1.4.6.pl \\\r\n  -sam frag_sopra.sam jump_sopra.sam -a .\/\r\n\r\n\u7a0b\u5e8f\u53c2\u6570\uff1a\r\n-sam string\r\n    \u8f93\u5165 sam \u6587\u4ef6\u3002\u591a\u4e2aillumina \u6587\u5e93\u7684sam\u6587\u4ef6\u7528\u7a7a\u683c\u9694\u5f00\u3002\r\n-a string\r\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u7684\u8def\u5f84\u3002\r\n<\/pre>\n
\u5f97\u5230sam\u6587\u4ef6\u5206\u6790\u540e\u7684\u7ed3\u679cfrag_sopra.sam_parsed\u548cjump_sopra.sam_parsed\u3002<\/p>\n
3.5 \u8fdb\u884c\u5e8f\u5217\u65b9\u5411\u548c\u8ddd\u79bb\u5206\u6790<\/h2>\n
\u8bfb\u53d6\u4e0a\u4e00\u6b65\u7b80\u5316\u540e\u7684sam\u6587\u4ef6\u4fe1\u606f\uff0c\u8fdb\u884c\u5206\u6790\u3002\u5f97\u5230contigs\u5e8f\u5217\u7684\u8986\u76d6\u5ea6\u3001library\u6587\u5e93\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\uff0c\u5e8f\u5217\u957f\u5ea6\u7b49\u3002<\/p>\n
\r\n$ \/opt\/biosoft\/SOPRA_v1.4.6\/source_codes_v1.4.6\/SOPRA_with_prebuilt_contigs\/s_read_parsed_sam_v1.4.6.pl \\\r\n  -parsed frag_sopra.sam_parsed -d 500 -parsed jump_sopra.sam_parsed -d 3000 -a .\/\r\n\r\n\u7a0b\u5e8f\u53c2\u6570\uff1a\r\n-parsed string\r\n    \u8f93\u5165 .sam_parsed \u6587\u4ef6\u3002\u82e5\u6709\u591a\u4e2a\u6587\u4ef6\uff0c\u5219\u7528\u7a7a\u683c\u5206\u5272\u3002\r\n-d int\r\n    illumina\u6570\u636e\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u3002\r\n-c int default: 5\r\n    \u5982\u679cread\u53ca\u5176\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u5728library\u4e2d\u51fa\u73b0\u7684\u6b21\u6570>=\u8be5\u503c\uff0c\u5219\u4e0d\u8ba1\u7b97\u5176\u6210\u5bf9\u4fe1\u606f\u3002\r\n    \u5728\u8fd0\u884c s_scaf_v1.4.6.pl \u7a0b\u5e8f\u540e\uff0c\u8f93\u5165\u65e5\u5fd7\u4e2d\u5f97\u5230\u5982\u4e0b\u4fe1\u606f\uff1a\r\n    Average number of links between two contigs using minlength 150 and minlink 2 is 63.38, ...\r\n    Starting cycle 1 of orientation assignment\r\n    Average number of links between two contigs using minlength 150 and minlink 4 is 184.84, ...\r\n    \u5982\u679c\u8be5\u503c(184.84)\u5927\u4e8e100\uff0c\u5219\u9700\u8981\u8003\u8651\u964d\u4f4e -c \u53c2\u6570\u7684\u503c\u3002\r\n    \u6b64\u5916\uff0c\u5982\u679c\u6570\u636e\u91cf\u6bd4\u8f83\u5c11\uff0c\u5e73\u5747\u8986\u76d6\u5ea6\u8f83\u4f4e\uff0c\u6bd4\u5982\u4f4e\u4e8e 10\uff0c\u5219\u8003\u8651\u589e\u52a0 -c \u53c2\u6570\u7684\u503c\u3002\r\n\r\n-e int default\uff1a0\r\n    \u5982\u679c\u8bbe\u7f6e\u5176\u503c\u4e3a 1\uff0c \u5219\u4f7f\u7528\u8f93\u5165\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u503c\u3002\u9ed8\u8ba4\u4e0b\u8f6f\u4ef6\u4f1a\u8ba1\u7b97\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u503c\uff0c\u5e76\u4f7f\u7528\u8f6f\u4ef6\u8ba1\u7b97\u51fa\u6765\u7684\u503c\u3002\r\n-a string\r\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u7684\u8def\u5f84\u3002\r\n<\/pre>\n
\u8f93\u51fa\u6587\u4ef6\u4e3a orientdistinfo_c5 \u3002 \u6b64\u5916\uff0c\u5728 div \u6587\u4ef6\u5939\u4e2d\u6709contigs\u5e8f\u5217\u7684\u8986\u76d6\u5ea6\u3001library\u6587\u5e93\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\uff0c\u5e8f\u5217\u957f\u5ea6\u7b49\u7edf\u8ba1\u4fe1\u606f\u3002<\/p>\n
3.6 \u8fdb\u884cscaffold\u8fde\u63a5<\/h2>\n
\r\n$ \/opt\/biosoft\/SOPRA_v1.4.6\/source_codes_v1.4.6\/SOPRA_with_prebuilt_contigs\/s_scaf_v1.4.6.pl \\\r\n  -o orientdistinfo_c5 -a .\/\r\n\r\n\u7a0b\u5e8f\u5e38\u7528\u53c2\u6570\uff1a\r\n-o string\r\n    \u8f93\u5165\u6587\u4ef6 orientdistinfo_c\u3002\r\n-w int default: 4\r\n    \u8fde\u63a52\u4e2acontigs\u6240\u9700\u8981\u7684\u6700\u5c0f\u7684pair links\u3002\r\n    \u5728\u8fd0\u884c s_scaf_v1.4.6.pl \u7a0b\u5e8f\u540e\uff0c\u8f93\u5165\u65e5\u5fd7\u4e2d\u5f97\u5230\u5982\u4e0b\u4fe1\u606f\uff1a\r\n    Average number of links between two contigs using minlength 150 and minlink 2 is 63.38, ...\r\n    Starting cycle 1 of orientation assignment\r\n    Average number of links between two contigs using minlength 150 and minlink 4 is 184.84, ...\r\n    \u5982\u679c\u8be5\u503c(184.84)\u5927\u4e8e100\uff0c\u5219\u9700\u8981\u8003\u8651\u63d0\u9ad8 -w \u53c2\u6570\u7684\u503c\u3002\u4e00\u822c -w \u53d6\u8be5\u503c\u7684 4~5%\u3002\u5982\u679c\u8be5\u503c\u8f83\u4f4e\uff0c\u6bd4\u5982\u4f4e\u4e8e10\u7684\u65f6\u5019\uff0c\u5219\u9700\u8981\u964d\u4f4e -w \u53c2\u6570\u7684\u503c\u3002\r\n-L int default: 150\r\n    \u7528\u4e8e\u8fde\u63a5scaffold\u7684\u6700\u5c0f\u957f\u5ea6\u7684contigs\u5e8f\u5217\u3002\r\n-h float default: 2.2\r\n    \u8bbe\u7f6e\u4e00\u4e2a\u7cfb\u6570\uff0c\u7528\u4e8e\u6392\u9664\u5bf9\u9ad8\u8986\u76d6\u5ea6contigs\u7684scaffold\u8fde\u63a5\u3002\u5927\u4e8e mean_coverage + h * std_coverage \u8be5\u8986\u76d6\u5ea6\u7684 contigs \uff0c\u4e0d\u80fd\u7528\u4e8escaffold\u8fde\u63a5\r\n-a string\r\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u7684\u8def\u5f84\u3002\r\n<\/pre>\n
\u7a0b\u5e8f\u8f93\u51fa\u6587\u4ef6\u4e3a scaffolds_h2.2_L150_w4.fasta \u3002\u8be5\u6587\u4ef6\u4e3a\u6700\u7ec8\u7684\u7ed3\u679c\u6587\u4ef6\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
1. SOPRA \u7b80\u4ecb SOPRA(Statistical Optimizati … \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],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2327"}],"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=2327"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2327\/revisions"}],"predecessor-version":[{"id":2328,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2327\/revisions\/2328"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2327"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2327"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2327"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}