{"id":2120,"date":"2014-06-09T21:40:28","date_gmt":"2014-06-09T13:40:28","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2120"},"modified":"2014-07-13T23:52:34","modified_gmt":"2014-07-13T15:52:34","slug":"%e4%bd%bf%e7%94%a8-sspace-%e8%bf%9b%e8%a1%8c-scaffoding","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2120","title":{"rendered":"\u4f7f\u7528 SSPACE \u8fdb\u884c scaffoding"},"content":{"rendered":"

SSPACE \u80fd\u5229\u7528 paired reads \u7684\u6bd4\u5bf9\u7ed3\u679c\uff0c\u5c06 contigs \u6216 scaffolds \u8fde\u63a5\u6210 scaffolds\u3002\u5176\u53c2\u8003\u6587\u732e\uff1aBoetzer M, Henkel C V, Jansen H J, et al. Scaffolding pre-assembled contigs using SSPACE[J]. Bioinformatics, 2011, 27(4): 578-579.<\/a><\/p>\n

1. \u5b89\u88c5 SSPACE<\/h1>\n

\u8f6f\u4ef6\u4e0b\u8f7d\u9875\u9762\uff1ahttp:\/\/www.baseclear.com\/lab-products\/bioinformatics-tools\/sspace-standard\/<\/a>\u3002<\/p>\n

\r\n$ tar zxf SSPACE-STANDARD-3.0_linux-x86_64.tar.gz\r\n$ .\/SSPACE-STANDARD-3.0_linux-x86_64\/SSPACE_Standard_v3.0.pl\r\n<\/pre>\n
\u89e3\u538b\u7f29\u8f6f\u4ef6\u5305\u540e\uff0c\u8fd0\u884c\u8f6f\u4ef6\u6587\u4ef6\u5939\u4e2d\u7684 perl \u7a0b\u5e8f\u5373\u53ef\u8fd0\u884c SSPACE\u3002\u8f6f\u4ef6\u4e3b\u76ee\u5f55\u4e0b\u5305\u542b\u4e00\u4e9b\u8f6f\u4ef6\u4f7f\u7528\u8bf4\u660e\u548c\u793a\u4f8b\u7b49,\u5176\u4e2d README \u6587\u4ef6\u63cf\u8ff0\u5f97\u975e\u5e38\u8be6\u7ec6\u3002<\/p>\n
2. SSPACE \u4f7f\u7528\u65b9\u6cd5<\/h1>\n
2.1 library \u6587\u4ef6<\/h2>\n
\u9996\u5148\u8981\u5efa\u7acb\u4e00\u4e2a\u63cf\u8ff0 library \u4fe1\u606f\u7684\u6587\u672c\u6587\u4ef6\uff0c\u4f8b\u5982\uff1a<\/p>\n
\r\nLib1 bwa file1.1.fasta file1.2.fasta 400 0.25 FR\r\nLib1 bowtie file2.1.fasta file2.2.fasta 400 0.25 FR\r\nLib2 bwasw file3.1.fastq file3.2.fastq 4000 0.5 RF\r\nLib2 TAB file4.tab 4000 0.5 RF\r\nLib3 TAB file5.tab 10000 0.5 RF\r\nunpaired bowtie unpaired_reads1.fasta\r\nunpaired bwasw unpaired_longreads1.gz\r\n<\/pre>\n
\u6b64 library \u6587\u4ef6\u7531\u591a\u5217\u7ec4\u6210\uff0c\u5217\u4e0e\u5217\u4e4b\u95f4\u7531 1 \u4e2a \u7a7a\u683c \u6216 tab \u5206\u9694\uff0c\u5404\u5217\u610f\u4e49\u5982\u4e0b\uff1a<\/p>\n
\r\n\u7b2c 1 \u5217\uff1a library \u540d\u79f0\u3002\u7a0b\u5e8f\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u4ea7\u751f\u7684\u4e34\u65f6\u6587\u4ef6\u4ee5\u6b64\u6765\u547d\u540d\uff1b \u591a\u4e2a\u884c\u53ef\u4ee5\u62e5\u6709\u540c\u4e00\u4e2a library \u540d\u79f0\uff0c\u5219\u5176\u5177\u6709\u76f8\u540c\u7684 library \u8bbe\u7f6e\u548c\u4e0d\u540c\u7684\u6570\u636e\u6587\u4ef6\uff1b \u540c\u65f6\uff0clibraries \u5fc5\u987b\u6309 insert size \u6765\u6392\u5e8f\uff0cinert size \u6700\u5c0f\u7684\u5fc5\u987b\u653e\u5230\u7b2c\u4e00\u884c\uff0c\u8fd9\u662f\u56e0\u4e3a\u8fdb\u884c scaffold \u6784\u5efa\u65f6\uff0c\u6309\u6b64\u6587\u4ef6\u63d0\u4f9b\u7684 libraries \u7684\u987a\u5e8f\u6765\u8f93\u5165\u6570\u636e\u7684\uff1b unpaired reads\uff0c \u5219\u7b2c\u4e00\u5217\u662f \u2018unpaired\u2019\u3002\r\n\u7b2c 2 \u5217\uff1a \u5c06 reads \u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u4e0a\u6240\u4f7f\u7528\u7684\u8f6f\u4ef6\u540d\uff0c \u53ef\u4ee5\u4e3a bowtie \u3001 bwa \u548c bwasw \u7b49\uff1b \u5982\u679c\u8f93\u5165\u7684\u6570\u636e\u662f reads \u6bd4\u5bf9\u8fc7\u540e\u7684 tab \u683c\u5f0f\u7ed3\u679c\uff0c\u5219\u6b64\u5217\u4e3a \u201cTAB\u201d\u3002\r\n\u7b2c 3\uff0c4 \u5217\uff1a Fasta \u6216 Fastq \u683c\u5f0f\u7684\u53cc\u672b\u7aef\u6d4b\u5e8f\u6587\u4ef6\uff0c\u5e76\u4e14\u6587\u4ef6\u4e2d\u6210\u5bf9\u7684 paired reads \u5fc5\u987b\u5728\u4e24\u4e2a\u6587\u4ef6\u4e2d\u5e76\u5904\u4e8e\u76f8\u540c\u7684\u884c\u53f7\u4e0a\uff0c\u540c\u65f6\uff0c\u8f6f\u4ef6\u8bfb\u53d6\u6570\u636e\u4e0e\u5e8f\u5217\u7684 headers \u65e0\u5173\u3002\u5982\u679c\u662f unpaired reads\uff0c\u5219\u4ec5\u9700\u8981\u7b2c 3 \u5217\uff0c\u4e3a tab \u683c\u5f0f\u7684 reads mapping \u7ed3\u679c\uff0c\u8fc7\u540e\u8be6\u8ff0\u3002\r\n\u7b2c 5,6 \u5217\uff1a\u7b2c 5 \u5217\u4e3a insert size \u7684\u671f\u671b\u503c\uff1b \u7b2c 6 \u5217\u4e3a insert size \u5141\u8bb8\u7684\u6700\u5c0f\u504f\u5dee\u3002 \u6bd4\u5982\uff0c\u8fd9\u4e24\u5217\u503c\u5206\u522b\u4e3a 4000 \u548c 0.5\uff0c\u5219 insert size \u5728 2000-6000 \u4e4b\u95f4\u7684 pairs \u624d\u662f\u6709\u6548 pairs\u3002\r\n\u7b2c 7 \u5217\uff1apaired-reads \u7684\u65b9\u5411\uff0c\u6709 FF\uff0cFR\uff0cRF \u6216 RR \u51e0\u79cd\u9009\u9879\u3002\r\n<\/pre>\n
2.2 \u7a0b\u5e8f\u53c2\u6570<\/h2>\n
\r\n-l \u8f93\u5165\u7684 library \u6587\u4ef6\r\n-s \u8f93\u5165\u7684 Fasta \u6587\u4ef6\r\n-x \u662f\u5426\u5bf9 contigs \u8fdb\u884c\u5ef6\u957f\u3002\u5176\u503c\u53ef\u4ee5\u4e3a 0 \u6216 1\u3002 1 \u8868\u793a\u8fdb\u884c\u5ef6\u4f38\uff0c0 \u8868\u793a\u4e0d\u5ef6\u4f38\u3002\u9ed8\u8ba4\u503c\u4e3a 0\u3002\r\n\r\n\u5ef6\u4f38\u53c2\u6570\uff1a\r\n-m \u8fdb\u884c\u5ef6\u4f38\u65f6\uff0cread \u548c\u57fa\u56e0\u7ec4\u5e8f\u5217\u6700\u5c0f\u7684 overlap\u3002\u6b64\u503c\u8d8a\u5927\uff0c\u5219\u7ed3\u679c\u8d8a\u51c6\u786e\uff0c\u540c\u65f6\u8017\u5185\u5b58\u8d8a\u5c11\u3002\u63a8\u8350\u6b64\u503c\u63a5\u8fd1\u6700\u957f\u7684 read \u7684\u957f\u5ea6\u3002\u6bd4\u5982\uff0c\u5bf9\u4e8e 26 bp \u957f\u5ea6\u7684 reads\uff0c \u8be5\u503c\u9002\u5408\u8bbe\u4e3a 32\uff5e35\u3002 \u9ed8\u8ba4\u6b64\u503c\u4e3a 32 \u3002\u6b64\u503c\u53d6\u503c\u8303\u56f4\u4e3a 15\uff5e50 \u3002\u8f6f\u4ef6\u8fd0\u884c\u65f6\uff0c\u5c06 unmapped reads \u5168\u90e8\u6253\u65ad\u6210 m+1 \u957f\u5ea6\u7684\u5e8f\u5217\uff0c\u8fd9\u4e9b\u5e8f\u5217\u7528\u4e8e\u8fdb\u884c contigs \u7684\u5ef6\u4f38\u3002\r\n-o \u8fdb\u884c\u5ef6\u4f38\u65f6\uff0c\u5ef6\u4f38 1 \u4e2a\u78b1\u57fa\u9700\u8981\u7684\u6700\u5c0f reads \u6570\u3002\u6b64\u503c\u8d8a\u5927\uff0c\u5219\u7ed3\u679c\u8d8a\u51c6\u786e\u3002\u9ed8\u8ba4\u503c\u4e3a 20 \u3002\r\n-r \u8fdb\u884c\u5ef6\u4f38\u65f6\uff0c\u5ef6\u4f38 1 \u4e2a\u78b1\u57fa\uff0c\u6b64\u78b1\u57fa\u5728\u6240\u6709\u5339\u914d\u7684 reads \u4e2d\u7684\u6700\u5c0f\u6bd4\u4f8b\u3002\u6b64\u503c\u8d8a\u5927\uff0c\u5219\u7ed3\u679c\u8d8a\u51c6\u786e\u3002\u9ed8\u8ba4\u503c\u4e3a 0.9 \u3002\r\n\r\nScaffolding \u53c2\u6570\uff1a\r\n-k \u5c06\u4e24\u4e2a contigs \u8fde\u63a5\u6210 scaffold \u65f6\uff0c\u9700\u8981\u7684\u6700\u5c0f\u7684 reads pairs \u6570\u76ee\u3002\u9ed8\u8ba4\u503c\u4e3a 5 \u3002\r\n-a \u5c06\u4e24\u4e2a contigs \u8fde\u63a5\u6210 scaffold \u65f6\uff0c\u8fd9\u4e24\u4e2a contigs \u4e4b\u95f4\u7684\u8fde\u63a5\u6570 \u4e0e \u5176\u548c\u5176\u5b83 contigs \u7684\u8fde\u63a5\u6570\u4e4b\u95f4\u7684\u6700\u5c0f\u6bd4\u503c\u3002\u6b64\u503c\u8d8a\u5927\uff0c\u5219\u7ed3\u679c\u8d8a\u51c6\u786e\u3002\u9ed8\u8ba4\u503c\u4e3a 0.70\r\n-n \u5728 scaffold \u4e2d\uff0c\u5c06\u4e24\u4e2a\u90bb\u8fd1\u7684 contigs \u5408\u5e76\u5230\u4e00\u8d77\u9700\u8981\u7684\u6700\u5c0f\u7684 overlap\u3002\u9ed8\u8ba4\u503c\u4e3a 15\u3002\r\n-z \u8fdb\u884c scaffolding \u65f6\uff0c\u5141\u8bb8\u7684\u6700\u5c0f\u7684 contig \u957f\u5ea6\u3002\u4f4e\u4e8e\u6b64\u957f\u5ea6\u7684 contig \u5c06\u4e0d\u80fd\u7528\u4e8e\u8fdb\u884c scaffold \u7ec4\u88c5\u3002\u9ed8\u8ba4\u503c\u4e3a 0 \u3002\u8f83\u957f\u7684 contigs \u4ea7\u751f\u7684 scaffolds \u6bd4\u8f83\u53ef\u4fe1\uff1b \u800c\u5c0f\u4e8e 100bp \u7684 contigs \u5bb9\u6613\u662f\u91cd\u590d\u5e8f\u5217\u3002\r\n\r\nbowtie \u6bd4\u5bf9\u53c2\u6570\uff1a\r\n-g \u4f7f\u7528 bowtie \u8fdb\u884c\u6bd4\u5bf9\u65f6\uff0c\u5141\u8bb8\u7684\u6700\u5927 gaps \u6570\u3002\u9ed8\u8ba4\u503c\u4e3a 0\r\n\r\n\u5176\u5b83\u53c2\u6570\uff1a\r\n-T \u8bbe\u5b9a\u8fd0\u884c\u7684\u7ebf\u7a0b\u6570\u3002\u9ed8\u8ba4\u503c\u4e3a 1\u3002\r\n-b \u8f93\u51fa\u6587\u4ef6\u5939\u540d\u53ca\u6587\u4ef6\u5939\u5185\u7684\u6587\u4ef6\u524d\u7f00\u3002\r\n-S \u5f53\u7a0b\u5e8f\u6b63\u5728\u8fd0\u884c\u65f6\uff0c\u8df3\u8fc7\u8bfb\u53d6 reads \u7684\u9636\u6bb5\u3002\u548c -b \u53c2\u6570\u7ed3\u5408\u4f7f\u7528\uff0c\u5219\u53ef\u4ee5\u540c\u65f6\u8fd0\u884c\u591a\u4e2a SSPACE \u7a0b\u5e8f\uff0c\u5bf9\u6bcf\u4e2a\u7a0b\u5e8f\u8bbe\u7f6e\u4e0d\u540c\u7684\u53c2\u6570\uff0c\u8fd9\u6837\u80fd\u8f83\u5feb\u5f97\u5230\u8f83\u597d\u7684\u7ed3\u679c\u3002\r\n-v verbose mode\r\n-p \u751f\u6210\u53ef\u4f9b\u53ef\u89c6\u5316\u7684 .dot \u6587\u4ef6\u3002\r\n<\/pre>\n
2.3 \u5176\u5b83\u5de5\u5177<\/h2>\n
SSPACE \u63d0\u4f9b\u4e86\u4e00\u4e9b\u5176\u5b83\u6bd4\u8f83\u6709\u7528\u7684\u5c0f\u5de5\u5177\uff1a<\/p>\n
\r\nestimate_insert_size.pl \u7528\u4e8e\u8ba1\u7b97 insert size\u3002\u6b64\u7a0b\u5e8f\u8ba1\u7b97\u7684\u7ed3\u679c\u6709\u4e9b\u95ee\u9898\u3002\r\nfastq_qualitytrim_pairs.pl \u5bf9 reads pairs \u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u7684\u7a0b\u5e8f\u3002\r\n<\/pre>\n
sam_bam2tab.pl \u5c06 bam sam \u6587\u4ef6\u8f6c\u6362\u4e3a tab \u683c\u5f0f\u7684\u7a0b\u5e8f\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
SSPACE \u80fd\u5229\u7528 paired reads \u7684\u6bd4\u5bf9\u7ed3\u679c\uff0c\u5c06 contigs  … \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\/2120"}],"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=2120"}],"version-history":[{"count":2,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2120\/revisions"}],"predecessor-version":[{"id":2243,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2120\/revisions\/2243"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2120"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2120"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2120"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}