{"id":2144,"date":"2014-06-10T20:54:09","date_gmt":"2014-06-10T12:54:09","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2144"},"modified":"2014-06-10T20:54:09","modified_gmt":"2014-06-10T12:54:09","slug":"%e4%bd%bf%e7%94%a8-edena-%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=2144","title":{"rendered":"\u4f7f\u7528 Edena \u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"<h1>1. \u7b80\u4ecb<\/h1>\n<p>Edena \u662f\u4e00\u4e2a\u57fa\u4e8e overlaps\u2013graph-based \u7684 de novo assembler\u3002\u4ec5\u80fd\u5f88\u597d\u5730\u4f7f\u7528 Illumina \u6570\u636e\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5\u3002\u8f6f\u4ef6\u80fd\u4f7f\u7528 direct-reverse (paired-ends) \u548c reverse-direct (mate-pairs) \u7684 Illumina \u6570\u636e\u3002\u540c\u65f6\u8981\u6c42 reads \u7684\u957f\u5ea6\u5fc5\u987b\u4e00\u81f4\uff0c\u5426\u5219\u6240\u6709 reads \u4f1a\u4ece 3&#8242; \u7aef\u5f00\u59cb\u622a\u77ed\u5230\u6700\u77ed\u7684 reads \u7684\u957f\u5ea6\u3002<\/p>\n<h1>2. Edena \u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/www.genomic.ch\/edena\/EdenaV3.131028.tar.gz\r\n$ tar zxf EdenaV3.131028.tar.gz -C\u3000\/opt\/biosoft\r\n$ cd \/opt\/biosoft\/EdenaV3.131028\/\r\n$ make\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/EdenaV3.131028\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<h1>3. Edena \u7684\u4f7f\u7528<\/h1>\n<p>\u8f6f\u4ef6\u76f4\u63a5\u4f7f\u7528 Edena \u547d\u4ee4\u5373\u53ef\u3002\u5305\u542b\u4e24\u4e2a\u6b65\u9aa4\uff1a overlapping \u548c assembling\u3002<\/p>\n<h2>3.1 overlapping<\/h2>\n<p>\u4f7f\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$ edena -nThreads 24 -DRpairs frag1_1.fq frag1_2.fq frag2_1.fq frag2_2.fq\\\r\n -RDpairs jump1_1.fq jump1_2.fq jump2_1.fq jump2_2.fq\r\n<\/pre>\n<p>\u6700\u540e\u7684\u7ed3\u679c\u6587\u4ef6\u4e3a out.ovl<\/p>\n<h2>3.2 Assembling<\/h2>\n<p>\u4f7f\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$ edena -e out.ovl\r\n<\/pre>\n<p>\u6700\u7ec8\u7684\u7ed3\u679c\u6587\u4ef6\u4e3a out_contigs.fasta \u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. \u7b80\u4ecb Edena \u662f\u4e00\u4e2a\u57fa\u4e8e overlaps\u2013graph-based \u7684 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2144\">\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\/2144"}],"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=2144"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2144\/revisions"}],"predecessor-version":[{"id":2145,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2144\/revisions\/2145"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2144"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2144"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2144"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}