{"id":2647,"date":"2018-12-20T00:24:12","date_gmt":"2018-12-19T16:24:12","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2647"},"modified":"2019-04-29T22:49:10","modified_gmt":"2019-04-29T14:49:10","slug":"%e4%bd%bf%e7%94%a8wtdbg2%e5%88%a9%e7%94%a8%e4%b8%89%e4%bb%a3%e6%95%b0%e6%8d%ae%e8%bf%9b%e8%a1%8c%e5%9f%ba%e5%9b%a0%e7%bb%84de-novo%e7%bb%84%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2647","title":{"rendered":"\u4f7f\u7528wtdbg2\u5229\u7528\u4e09\u4ee3\u6570\u636e\u8fdb\u884c\u57fa\u56e0\u7ec4de novo\u7ec4\u88c5"},"content":{"rendered":"<h1>wtdbg2\u8f6f\u4ef6\u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h1>\n<pre>$ wget https:\/\/github.com\/ruanjue\/wtdbg2\/archive\/v2.4.tar.gz -O ~\/software_packages\/wtdbg-v2.4.tar.gz\n$ tar zxf \/share\/disk02_8T\/home\/chenlianfu\/software_packages\/wtdbg-v2.2.tar.gz -C \/opt\/biosoft\/\n$ cd \/opt\/biosoft\/wtdbg2-2.4\/\n$ make -j 4\n$ echo 'PATH=$PATH:\/opt\/biosoft\/wtdbg2-2.4' &gt;&gt; ~\/.bashrc\n$ source ~\/.bashrc\n<\/pre>\n<h1>wtdbg2\u8f6f\u4ef6\u4f7f\u7528<\/h1>\n<pre>\u8fdb\u884c\u57fa\u56e0\u7ec4\u88c5\n$ wtdbg2 -t 16 -i reads.fa.gz -fo prefix -L 5000\n\n\u5f97\u5230\u4e00\u81f4\u6027\u5e8f\u5217\n$ wtpoa-cns -t 16 -i prefix.ctg.lay -fo prefix.ctg.lay.fa\n\n\u5229\u7528\u4e09\u4ee3reads\u7684\u6bd4\u5bf9\u7ed3\u679c\u5bf9\u57fa\u56e0\u7ec4\u5e8f\u5217\u8fdb\u884c\u6253\u78e8\u4fee\u6b63\n$ minimap2 -t 16 -x map-pb -a prefix.ctg.lay.fa reads.fa.gz | samtools view -Sb - &gt;prefix.ctg.lay.map.bam\n$ samtools sort prefix.ctg.lay.map.bam prefix.ctg.lay.map.srt\n$ samtools view prefix.ctg.lay.map.srt.bam | .\/wtpoa-cns -t 16 -d prefix.ctg.lay.fa -i - -fo prefix.ctg.lay.2nd.fa\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>wtdbg2\u8f6f\u4ef6\u4e0b\u8f7d\u4e0e\u5b89\u88c5 $ wget https:\/\/github.com\/ &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2647\">\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\/2647"}],"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=2647"}],"version-history":[{"count":3,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2647\/revisions"}],"predecessor-version":[{"id":2878,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2647\/revisions\/2878"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2647"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2647"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2647"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}