{"id":2112,"date":"2014-06-09T21:29:47","date_gmt":"2014-06-09T13:29:47","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2112"},"modified":"2014-12-31T04:54:13","modified_gmt":"2014-12-30T20:54:13","slug":"%e4%bd%bf%e7%94%a8platanus%e8%bf%9b%e8%a1%8c%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%bb%84%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2112","title":{"rendered":"\u4f7f\u7528Platanus\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"<h1>1. platanus \u7684\u5b89\u88c5<\/h1>\n<pre>\r\n$ mkdir \/opt\/biosoft\/platanus\r\n$ wget http:\/\/platanus.bio.titech.ac.jp\/Platanus_release\/20130901010201\/platanus -P \/opt\/biosoft\/platanus\r\n$ wget http:\/\/platanus.bio.titech.ac.jp\/Platanus_release\/20130901010201\/README -P \/opt\/biosoft\/platanus\r\n$ chmod 755 \/opt\/biosoft\/platanus\r\n<\/pre>\n<p>\u4e0b\u8f7d\u7684\u4e24\u4e2a\u6587\u4ef6\u5206\u522b\u662f\u4e3b\u7a0b\u5e8f\u548c\u8bf4\u660e\u6587\u4ef6\u3002<\/p>\n<h1>2. platanus \u7684\u4f7f\u7528<\/h1>\n<p>platanus \u4e0b\u5305\u542b\u4e09\u4e2a\u547d\u4ee4\uff0c\u5206\u522b\u662f assemble\uff0c scaffold\uff0c gap_close \u3002\u5176\u7528\u6cd5\u5982\u4e0b\uff1a\u4e2a<br \/>\n\u8fd9 3 \u4e2a\u547d\u4ee4\u7684\u5171\u540c\u53c2\u6570\u4e3a\uff1a<\/p>\n<pre>\r\n-t \u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\uff0c\u6b64\u503c<=100\uff0c\u9ed8\u8ba4\u503c\u4e3a 1 \u3002\r\n-o \u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\uff0c\u9ed8\u8ba4\u503c\u4e3a out \u3002\r\n<\/pre>\n<h2>2.1 assemble<\/h2>\n<p>\u6b64\u547d\u4ee4\u57fa\u4e8e Bruign \u56fe\u7684\u7b97\u6cd5\u6765\u7ec4\u88c5\u51fa contig<\/p>\n<pre>\r\n-f FILE1 [File2 ...]\r\n\u8f93\u5165\u7684\u6587\u4ef6\uff0c\u652f\u6301\u8f93\u5165\u7684\u6587\u4ef6\u603b\u8f93\u5165\u6700\u5927\u4e3a 100 \u3002\u6587\u4ef6\u53ef\u4ee5\u4e3a fasta \u6216 fastq \u683c\u5f0f\u3002 \u8f6f\u4ef6\u4f1a\u81ea\u52a8\u8bc6\u522b\u5176\u683c\u5f0f\u3002\u4e0d\u4f1a\u8fd0\u7528\u5230\u78b1\u57fa\u8d28\u91cf\u503c\uff0c\u78b1\u57fa\u8d28\u91cf\u503c\u5bf9\u7ec4\u88c5\u65e0\u4efb\u4f55\u5f71\u54cd\u3002\r\n-k INT\r\n\u521d\u59cb\u7684 k-mer \u5927\u5c0f\uff0c\u9ed8\u8ba4\u503c\u4e3a 32 \u3002\u6570\u636e\u8986\u76d6\u5ea6\u4f4e\u65f6\uff0c\u8be5\u503c\u8981\u8bbe\u5c0f\u4e9b\u3002\r\n-s INT\r\nk-mer \u503c\u7684\u6b65\u8fdb\u3002\u6b64\u503c\u5fc5\u987b >= 1\uff0c\u9ed8\u8ba4\u503c\u4e3a 10 \u3002\u7a0b\u5e8f\u4f1a\u4f7f\u7528\u591a\u4e2a K-mer \u503c\u8fdb\u884c contigs \u7ec4\u88c5\u3002\r\n-n INT\r\n\u521d\u59cb\u7684 k-mer \u8986\u76d6\u5ea6\u7684 cutoff\u3002 \u9ed8\u8ba4\u503c\u4e3a 0\uff0c\u5373\u81ea\u52a8\u53d6\u503c\u3002\u81ea\u52a8\u53d6\u503c\u4f9d\u8d56\u4e8e k-mer \u7684\u9891\u7387\u5206\u5e03\u3002\u5982\u679c\u5176\u5206\u5e03\u4e0d\u6b63\u5e38\uff0c\u5219\u5e94\u8be5\u624b\u52a8\u8bbe\u7f6e\u3002\r\n-c INT\r\n\u8bbe\u7f6e\u6700\u5c0f\u7684 k-mer \u8986\u76d6\u5ea6\u3002\u9ed8\u8ba4\u503c\u4e3a 2 \u3002\u5728 k-mer \u503c\u8d8a\u5927\u7684\u65f6\u5019\uff0c\u5219 k-mer \u8986\u76d6\u5ea6\u8d8a\u5c0f\uff0c\u5176 cutoff \u503c\u8d8a\u5c0f\uff0c\u4f46\u6b64 cutoff \u503c\u4e0d\u80fd\u4f4e\u4e8e\u6b64\u53c2\u6570\u8bbe\u7f6e\u7684\u503c\u3002\r\n-a FLOAT\r\nK-mer \u503c\u589e\u5927\u7684\u5b89\u5168\u6027\u6c34\u5e73\uff0c\u9ed8\u8ba4\u503c\u4e3a 10.0 \u3002\u589e\u5927\u6700\u7ec8\u7684 k-mer \u503c\u3002\u5982\u679c\u727a\u7272\u51c6\u786e\u6027\u6765\u5ef6\u4f38 contig\uff0c\u5219\u8bbe\u7f6e\u8f83\u4f4e\u7684\u503c\uff0c\u6bd4\u5982\u4e3a 5.0 \u3002\r\n-u FLOAT\r\n\u6d88\u9664\u6c14\u6ce1\u6240\u8fd0\u884c\u7684\u6700\u5927\u5dee\u5f02\uff0c\u9ed8\u8ba4\u503c\u4e3a 0.1 \u3002\u6b64\u503c\u8d8a\u5927\uff0c\u5219\u8d8a\u5bb9\u6613\u6d88\u9664\u6c14\u6ce1\u3002\u7279\u522b\u662f\u57fa\u56e0\u7ec4\u6742\u5408\u7387\u9ad8\u65f6\uff0c\u6b64\u503c\u63a8\u8350\u8bbe\u7f6e\u66f4\u9ad8\uff0c\u6bd4\u5982\u4e3a 0.2 \u3002\r\n-d FLOAT\r\n\u5f53\u5206\u652f\u7684\u8986\u76d6\u7387\u8d85\u8fc7\u6b64\u503c\u65f6\uff0c\u5219\u622a\u65ad\u5206\u652f\uff0c\u9ed8\u8ba4\u503c\u4e3a 0.5 \u3002\u6b64\u503c\u8d8a\u5c0f\uff0c\u5219\u51c6\u786e\u7387\u8d8a\u9ad8\u3002\u5982\u679c\u78b1\u57fa\u9519\u8bef\u7387\u8f83\u4f4e\uff0c\u5219\u9002\u5408\u8bbe\u7f6e\u8f83\u4f4e\u7684\u503c\uff0c\u6bd4\u5982 0.3 \u3002\r\n-m INT\r\n\u9650\u5236\u5185\u5b58\uff0c\u5355\u4f4d\u4e3a GB\uff0c\u9ed8\u8ba4\u503c\u4e3a 16 \u3002\u5f53\u7a0b\u5e8f\u9700\u8981\u6d88\u8017\u7684\u5185\u5b58\u8d85\u8fc7\u6b64\u503c\uff0c\u5219\u4f1a\u63d0\u793a\u8b66\u544a\uff0c\u4f46\u4e0d\u4f1a\u4e2d\u65ad\u8fd0\u884c\u3002\r\n<\/pre>\n<p>\u6b64\u7a0b\u5e8f\u8f93\u51fa\u7684\u6587\u4ef6\u4e3a<\/p>\n<pre>\r\nPREFIX_contig.fa  \u7ec4\u88c5\u51fa\u7684\u8fde\u7eed\u7684\u5e8f\u5217\r\nPREFIX_contigBubble.fa  \u878d\u5408\u5e76\u5220\u9664\u7684\u6c14\u6ce1\u5e8f\u5217\r\nPREFIX_kmerFrq.tsv  k-mers \u9891\u6570\u7684\u5206\u5e03\r\n<\/pre>\n<h2>2.2 scaffold<\/h2>\n<p>scaffold \u7528\u4e8e\u5c06 paired reads \u6bd4\u5bf9\u5230 contigs \u4e0a\uff0c\u5e76\u786e\u5b9a contigs \u7684\u987a\u5e8f\u548c\u65b9\u5411\uff0c\u6784\u5efa\u51fa scaffolds \u3002<\/p>\n<pre>\r\n-c FILE1 [FILE2 ...]\r\ncontig \u6587\u4ef6\u3002 \u5728\u6b64 fasta \u6587\u4ef6\u7684 header \u4e2d\uff0c\u7a0b\u5e8f\u8bc6\u522b\u5b57\u7b26 \u2018cov\u2019\u5e76\u5c06\u5176\u540e\u7684\u6570\u503c\u4f5c\u4e3a\u8986\u76d6\u5ea6\u7684\u503c\u3002\u5373\u4f7f\u6ca1\u6709 cov \u4fe1\u606f\uff0c\u7a0b\u5e8f\u4e5f\u80fd\u5904\u7406\u3002\r\n-b FILE1 [FILE2 ...]\r\nBubble_seq_file\r\n-ip{INT} PAIR1 [PAIR2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0\uff0c\u540e\u63a5 Inward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5728\u540c\u4e00\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e2a\u6587\u4ef6\u540d\u3002\r\n-IP{INT} FWD1 REV1 [FWD2 REV2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0, \u540e\u63a5 Inward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5206\u522b\u4f4d\u4e8e\u4e24\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e24\u4e2a\u6587\u4ef6\u540d\u3002\r\n-op{INT} PAIR1 [PAIR2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0\uff0c\u540e\u63a5 Outward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5728\u540c\u4e00\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e2a\u6587\u4ef6\u540d\u3002\r\n-OP{INT} FWD1 REV1 [FWD2 REV2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0, \u540e\u63a5 Outward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5206\u522b\u4f4d\u4e8e\u4e24\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e24\u4e2a\u6587\u4ef6\u540d\u3002\r\n-n{INT1} INT2\r\nINT1 \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0\uff0c INT2 \u662f\u6700\u5c0f\u7684 insert size \u3002 \u5728\u8fdb\u884c scaffolding \u65f6\uff0c\u7a0b\u5e8f\u4f1a\u81ea\u52a8\u4f30\u7b97\u5404\u4e2a\u6587\u5e93\u7684 insert size \u503c\u3002\u5982\u679c\u6587\u5e93\u4e2d paired reads \u4f30\u7b97\u51fa\u7684 insert size < IN2\uff0c\u5219\u820d\u5f03\u6b64 paired reads \u4fe1\u606f\u3002\r\n-a{INT1} INT2\r\nINT1 \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0\uff0c INT2 \u662f\u8bbe\u5b9a\u7684 insert size \u7684\u5e73\u5747\u503c \u3002\u8bbe\u5b9a\u6b64\u53c2\u6570\uff0c\u5219\u7a0b\u5e8f\u4e0d\u8fdb\u884c\u81ea\u52a8\u4f30\u7b97 insert size \u3002\r\n-d{INT1} INT2\r\nINT1 \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0\uff0c INT2 \u662f\u8bbe\u5b9a\u7684 insert size \u7684\u6807\u51c6\u5dee\u3002\u8bbe\u5b9a\u6b64\u53c2\u6570\uff0c\u5219\u7a0b\u5e8f\u4e0d\u8fdb\u884c\u81ea\u52a8\u4f30\u7b97 insert size \u3002\r\n-s INT\r\nMapping seed length (default 32)\u3002\u6b64\u503c\u8bbe\u5b9a\u4e0d\u80fd\u8d85\u8fc7 reads \u7684\u957f\u5ea6\u3002\u8d8a\u5c0f\uff0c\u5219\u7a0b\u5e8f\u8fd0\u884c\u901f\u5ea6\u8d8a\u4f4e\u3002\r\n-v INT\r\n\u6700\u5c0f\u7684\u91cd\u53e0\u957f\u5ea6(default 32)\u3002 \u5982\u679c\u4e34\u8fd1\u7684 contigs \u91cd\u53e0\u7684\u957f\u5ea6 >= INT\uff0c\u5219\u8fd9\u4e24\u4e2a contigs \u5219\u8fde\u63a5\u8d77\u6765\u3002\r\n-l INT\r\n\u8fde\u63a5\u4e24\u4e2a contig \u6240\u9700\u8981\u7684\u6700\u5c0f\u7684 paired reads \u7684\u8fde\u63a5\u6570\u3002\r\n-u FLOAT\r\n\u6d88\u9664\u6c14\u6ce1\u6240\u8fd0\u884c\u7684\u6700\u5927\u5dee\u5f02\uff0c\u9ed8\u8ba4\u503c\u4e3a 0.1 \u3002\u6b64\u503c\u8d8a\u5927\uff0c\u5219\u8d8a\u5bb9\u6613\u6d88\u9664\u6c14\u6ce1\u3002\u7279\u522b\u662f\u57fa\u56e0\u7ec4\u6742\u5408\u7387\u9ad8\u65f6\uff0c\u6b64\u503c\u63a8\u8350\u8bbe\u7f6e\u66f4\u9ad8\uff0c\u6bd4\u5982\u4e3a 0.2 \u3002\r\n<\/pre>\n<p>\u6b64\u7a0b\u5e8f\u7684\u8f93\u51fa\u6587\u4ef6\uff1a<\/p>\n<pre>\r\nPREFIX_scaffold.fa  \u7ec4\u88c5\u51fa\u6765\u7684 scaffold \u5e8f\u5217\r\nPREFIX_scaffoldBubble.fa  \u53bb\u9664\u7684 bubble \u5e8f\u5217\r\nPREFIX_scaffoldComponent.tsb  scaffold \u7531\u76f8\u5e94\u7684 contigs \u7ec4\u6210\u7684\u4fe1\u606f\r\n<\/pre>\n<h2>2.3 gap_close<\/h2>\n<p>\u7a0b\u5e8f\u5c06 paired reads \u6bd4\u5bf9\u5230 scaffolds\uff0c\u5c06 reads \u5b9a\u4f4d\u5230 gaps \u4e0a\uff0c\u5e76\u5173\u95ed\u4e00\u4e9b gap \u3002<\/p>\n<pre>\r\n-c FILE1 [FILE2 ...]\r\nscaffold \u6587\u4ef6\r\n-ip{INT} PAIR1 [PAIR2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0\uff0c\u540e\u63a5 Inward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5728\u540c\u4e00\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e2a\u6587\u4ef6\u540d\u3002\r\n-IP{INT} FWD1 REV1 [FWD2 REV2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0, \u540e\u63a5 Inward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5206\u522b\u4f4d\u4e8e\u4e24\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e24\u4e2a\u6587\u4ef6\u540d\u3002\r\n-op{INT} PAIR1 [PAIR2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0\uff0c\u540e\u63a5 Outward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5728\u540c\u4e00\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e2a\u6587\u4ef6\u540d\u3002\r\n-OP{INT} FWD1 REV1 [FWD2 REV2 ...]\r\nINT \u5728\u53c2\u6570\u7684\u540d\u79f0\u4e2d\uff0c\u662f LIB \u7684\u540d\u79f0, \u540e\u63a5 Outward Paired \u7684\u6570\u636e\u6587\u4ef6\u3002\u9996\u5c3e reads \u5206\u522b\u4f4d\u4e8e\u4e24\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6b64\u53c2\u6570\u540e\u63a5\u8fd9\u4e24\u4e2a\u6587\u4ef6\u540d\u3002\r\n-s INT\r\nMapping seed length (default 32)\u3002\u6b64\u503c\u8bbe\u5b9a\u4e0d\u80fd\u8d85\u8fc7 reads \u7684\u957f\u5ea6\u3002\u8d8a\u5c0f\uff0c\u5219\u7a0b\u5e8f\u8fd0\u884c\u901f\u5ea6\u8d8a\u4f4e\u3002\r\n-v INT\r\n\u6700\u5c0f\u7684\u91cd\u53e0\u957f\u5ea6(default 32)\u3002 \u6b64\u503c\u8d8a\u5c0f\uff0c\u4f8b\u5982 20\uff0c\u5219\u5173\u95ed\u7684 gap \u4f1a\u8d8a\u591a\u3002\r\n-e FLOAT\r\n\u91cd\u53e0\u533a\u6240\u5141\u8bb8\u7684\u6700\u4f4e\u9519\u8bef\u7387\uff0c\u9ed8\u8ba4\u503c\u4e3a 0.05 \u3002 \u6b64\u503c\u8d8a\u5927\uff0c\u4f8b\u5982 0.1 \uff0c\u5219\u5173\u95ed\u7684 gap \u4f1a\u8d8a\u591a\u3002\r\n<\/pre>\n<p>\u7a0b\u5e8f\u8f93\u51fa\u7684\u6587\u4ef6\uff1a<\/p>\n<pre>\r\nPREFIX_gapClosed.fa  \u8865\u6d1e\u540e\u7684\u5e8f\u5217\u6587\u4ef6\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. platanus \u7684\u5b89\u88c5 $ mkdir \/opt\/biosoft\/pla &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2112\">\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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2112"}],"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=2112"}],"version-history":[{"count":2,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2112\/revisions"}],"predecessor-version":[{"id":2256,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2112\/revisions\/2256"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2112"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2112"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2112"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}