{"id":2114,"date":"2014-06-09T21:35:12","date_gmt":"2014-06-09T13:35:12","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2114"},"modified":"2014-06-09T21:35:12","modified_gmt":"2014-06-09T13:35:12","slug":"%e4%bd%bf%e7%94%a8-pasha-%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=2114","title":{"rendered":"\u4f7f\u7528 PASHA \u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"<h1>1. PASHA \u7b80\u4ecb<\/h1>\n<p>\u5e76\u884c\u5316\u8fd0\u7b97\uff0c\u901f\u5ea6\u5feb\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\u3002<\/p>\n<h1>2. PASHA \u7684\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/cznic.dl.sourceforge.net\/project\/pasha\/Pasha-1.0.10.tar.bz2\r\n$ tar jxf Pasha-1.0.10.tar.bz2 -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/Pasha-1.0.10\/\r\n\u5b89\u88c5 PASHA \u524d\u9700\u8981\u5b89\u88c5 TBB\r\n$ wget www.threadingbuildingblocks.org\/sites\/default\/files\/software_releases\/linux\/tbb42_20140416oss_lin.tgz\r\n$ tar zxf tbb42_20140416oss_lin.tgz\r\n\u4fee\u6539 Pasha \u8f6f\u4ef6\u7684 Makefile \u6587\u4ef6\u4e2d TBB \u6587\u4ef6\u5939\u8def\u5f84\u7684\u6307\u5411\r\n$ perl -p -i -e 's#~\/install#\/opt\/biosoft\/Pasha-1.0.10\/tbb42_20140416oss#' Makefile\r\n$ make\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/Pasha-1.0.10\/bin' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<h1>2. \u7a0b\u5e8f\u7684\u53c2\u6570<\/h1>\n<h2>2.1 pasha-kmergen<\/h2>\n<p>\u6b64\u547d\u4ee4\u7528\u4e8e\u751f\u6210 k-mers\u3002\u8f93\u5165\u6587\u4ef6\u53ef\u4ee5\u4e3a fasta \u6216 fastq \u6587\u4ef6\u3002<br \/>\n\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-fasta str\r\n\u8f93\u5165 fasta \u683c\u5f0f\u7684\u6570\u636e\r\n-fastq str\r\n\u8f93\u5165 fastq \u683c\u5f0f\u7684\u6570\u636e\r\n-k int\r\n\u8f93\u5165 k-mer size\uff0c\u4ece 1 \u5230 31 \u7684\u5947\u6570\uff0c\u9ed8\u8ba4\u503c\u4e3a 21\r\n<\/pre>\n<p>\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$ pasha-kmergen DIRECTORY -fasta in.fasta -k KMER_SIZE\r\n$ pasha-kmergen DIRECTORY -fasta in.fasta -fasta in2.fasta -k KMER_SIZE\r\n$ pasha-kmergen DIRECTORY -fasta in.fasta -fastq in2.fastq -k KMER_SIZE\r\n$ mpirun -np 8 pasha-kmergen DIRECTORY -fasta in.fasta -k KMER_SIZE\r\n<\/pre>\n<p>\u6bcf\u4e2a pasha-kmergen \u4f7f\u7528 2 \u4e2a\u7ebf\u7a0b\u3002\u56e0\u6b64\uff0c\u63a8\u8350 -np \u5bf9\u5e94\u7684\u503c\u6700\u597d\u4f4e\u4e8e CPU cores \u7684\u4e00\u534a\u3002<\/p>\n<h2>2.2 pasha-pregraph<\/h2>\n<p>\u6b64\u547d\u4ee4\u7528\u4e8e\u5229\u7528 k-mers \u6765\u6784\u5efa\u521d\u6b65\u7684 de Bruijn \u56fe\uff0c\u518d\u53bb\u9664 tips \u548c low-coverage paths\u3002<br \/>\n\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-fasta str\r\n\u8f93\u5165 fasta \u683c\u5f0f\u7684\u6570\u636e\r\n-fastq str\r\n\u8f93\u5165 fastq \u683c\u5f0f\u7684\u6570\u636e\r\n<\/pre>\n<p>\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$ pasha-pregraph DIRECTORY -fasta in.fasta\r\n$ pasha-pregraph DIRECTORY -fasta in.fasta -fasta in2.fasta\r\n$ pasha-pregraph DIRECTORY -fasta in.fasta -fastq in2.fastq\r\n$ mpirun -np 8 pasha-pregraph DIRECTORY -fasta in.fasta\r\n<\/pre>\n<p>\u5f53\u4f7f\u7528 MPI \u8fdb\u884c\u5e76\u884c\u8fd0\u7b97\u662f\uff0cpasha-pregraph \u548c pasha-kmergen \u4f7f\u7528 -np \u6307\u5b9a\u7684\u7ebf\u7a0b\u6570\u8981\u4e00\u81f4\u3002<\/p>\n<h2>2.3 pasha-graph<\/h2>\n<p>\u6b64\u547d\u4ee4\u7528\u4e8e\u878d\u5408 bubbles\uff0c\u751f\u6210 contigs\uff0c\u5e76\u8fdb\u884c scaffolding\u3002<br \/>\n\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-fasta str\r\n\u8f93\u5165 fasta \u683c\u5f0f\u7684\u6570\u636e\u3002\u7a0b\u5e8f\u8bc6\u522b\u6b64\u6570\u636e\u4e3a\u5355\u7aef\u6570\u636e\u3002\r\n-fastq str\r\n\u8f93\u5165 fastq \u683c\u5f0f\u7684\u6570\u636e\u3002\u7a0b\u5e8f\u8bc6\u522b\u6b64\u6570\u636e\u4e3a\u5355\u7aef\u6570\u636e\u3002\r\n-fastaPaired str\r\n\u8f93\u5165 fasta \u683c\u5f0f\u7684\u6570\u636e\u3002\u540e\u63a5\u4e24\u4e2a\u7528\u7a7a\u683c\u5206\u9694\u7684\u6587\u4ef6\u3002\u7a0b\u5e8f\u8bc6\u522b\u6b64\u6570\u636e\u4e3a\u53cc\u7aef\u6570\u636e\u3002\r\n-fastqPaired str\r\n\u8f93\u5165 fastq \u683c\u5f0f\u7684\u6570\u636e\u3002\u540e\u63a5\u4e24\u4e2a\u7528\u7a7a\u683c\u5206\u9694\u7684\u6587\u4ef6\u3002\u7a0b\u5e8f\u8bc6\u522b\u6b64\u6570\u636e\u4e3a\u53cc\u7aef\u6570\u636e\u3002\r\n-fastaPairedFile str\r\n\u8f93\u5165 fasta \u683c\u5f0f\u7684\u6570\u636e\u3002\u540e\u63a5 1 \u4e2a\u6587\u4ef6\uff0c\u6b64\u6587\u4ef6\u662f\u53cc\u7aef\u6570\u636e\u4ea4\u53c9\u6574\u5408\u7684\u7ed3\u679c\u3002\u7a0b\u5e8f\u8bc6\u522b\u6b64\u6570\u636e\u4e3a\u53cc\u7aef\u6570\u636e\u3002\r\n-fastqPairedFile str\r\n\u8f93\u5165 fastq \u683c\u5f0f\u7684\u6570\u636e\u3002\u540e\u63a5 1 \u4e2a\u6587\u4ef6\uff0c\u6b64\u6587\u4ef6\u662f\u53cc\u7aef\u6570\u636e\u4ea4\u53c9\u6574\u5408\u7684\u7ed3\u679c\u3002\u7a0b\u5e8f\u8bc6\u522b\u6b64\u6570\u636e\u4e3a\u53cc\u7aef\u6570\u636e\u3002\r\n-numthreads int\r\n\u7ebf\u7a0b\u6570\uff0c\u9ed8\u8ba4\u503c\u4e3a 1\u3002\r\n<\/pre>\n<p>\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n\u4e0d\u8fdb\u884c scaffolding\uff1a\r\n$ pasha-graph DIRECTORY -fasta in.fasta\r\n$ pasha-graph DIRECTORY -fasta in.fasta -fasta in2.fasta\r\n$ pasha-graph DIRECTORY -fasta in.fasta -fastq in2.fastq\r\n$ pasha-graph DIRECTORY -fasta in.fasta -numthreads 4\r\n\u8fdb\u884c scaffolding\uff1a\r\n$ pasha-graph DIRECTORY -fastaPaired in_1.fasta in_2.fasta\r\n$ pasha-graph DIRECTORY -fastaPaired in_1.fasta in_2.fasta -fastaPaired in2_1.fasta in2_2.fasta\r\n$ pasha-graph DIRECTORY -fastqPaired in_1.fastq in_2.fastq -numthreads 4\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. PASHA \u7b80\u4ecb \u5e76\u884c\u5316\u8fd0\u7b97\uff0c\u901f\u5ea6\u5feb\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\u3002 2. PASHA  &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2114\">\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\/2114"}],"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=2114"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2114\/revisions"}],"predecessor-version":[{"id":2115,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2114\/revisions\/2115"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2114"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2114"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2114"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}