{"id":2109,"date":"2014-06-09T21:28:13","date_gmt":"2014-06-09T13:28:13","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2109"},"modified":"2014-06-09T21:28:13","modified_gmt":"2014-06-09T13:28:13","slug":"%e4%bd%bf%e7%94%a8abyss%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=2109","title":{"rendered":"\u4f7f\u7528ABySS\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"<h1>1. ABySS\u7684\u5b89\u88c5<\/h1>\n<pre>\r\n\u5b89\u88c5google-sparsehash\r\n$ sudo rpm -ivh http:\/\/sparsehash.googlecode.com\/files\/sparsehash-2.0.2-1.noarch.rpm\r\n\r\n$ wget http:\/\/www.bcgsc.ca\/platform\/bioinfo\/software\/abyss\/releases\/1.3.7\/abyss-1.3.7.tar.gz\r\n$ tar zxf abyss-1.3.7.tar.gz\r\n$ cd abyss-1.3.7\/\r\n$ .\/configure --prefix=\/opt\/biosoft\/abyss-1.3.7\/ && make -j 4 && make install\r\n\u9ed8\u8ba4\u4e0bABySS\u652f\u6301\u7684\u6700\u5927Kmer\u662f64\uff0c\u5728 configure \u4e2d\u4f7f\u7528 --enable-maxk=96 \u6539\u53d8\u8f6f\u4ef6\u6240\u80fd\u652f\u6301\u7684\u6700\u5927 kmer \u957f\u5ea6\u3002\r\n$ make\r\n$ make install\r\n\r\n$ cd ..\r\n$ rm abyss-1.3.7\/ -rf\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/abyss-1.3.7\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<h1>2. ABySS\u7684\u4f7f\u7528<\/h1>\n<p>\u4f7f\u7528 ABYSS \u547d\u4ee4\u80fd\u5c06 short reads \u7ec4\u88c5\u6210 contigs\u3002\u800c\u5982\u679c\u9700\u8981\u7ec4\u88c5\u6210 scaffolds\uff0c\u5219\u9700\u8981\u4f7f\u7528 abyss-pe \u547d\u4ee4\u3002<\/p>\n<h2>2.1 \u4f7f\u7528 ABYSS \u5c06 short reads \u7ec4\u88c5\u6210 contigs<\/h2>\n<p>\u4f7f\u7528\u5982\u4e0b\u547d\u4ee4\u67e5\u9605 ABYSS \u547d\u4ee4\u7684\u8bf4\u660e\uff1a<\/p>\n<pre>\r\n$ ABYSS --help\r\n\u6216\u8005\r\n$ less \/opt\/biosoft\/abyss-1.3.7\/share\/man\/man1\/ABYSS.1\r\n<\/pre>\n<p>\u7b80\u8981\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n<pre>\r\n$ ABYSS -k 31 -o 31_contigs.fa read1.fastq reads2.fastq\r\n\u6ce8\u610f\u4e8b\u9879\uff1a -k \u548c -o \u53c2\u6570\u662f\u5fc5\u987b\u53c2\u6570\uff1b \u8f93\u5165\u6587\u4ef6\u53ef\u4ee5\u6709\u591a\u4e2a\u3002\r\n<\/pre>\n<p>\u4e3b\u8981\u4f7f\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\n--chastity\r\n    \u53bb\u9664\u6c61\u67d3\u7684reads\uff0c\u8fd9\u662f\u9ed8\u8ba4\u9009\u9879\u3002\r\n--no-chastity\r\n    \u4e0d\u53bb\u9664\u6c61\u67d3\u7684reads\u3002\r\n--trim-masked\r\n    \u4ece\u5e8f\u5217\u67d0\u7aef\u53bb\u9664\u4f4e\u8d28\u91cf\u7684\u78b1\u57fa\uff0c\u8fd9\u662f\u9ed8\u8ba4\u9009\u9879\u3002\r\n--no-trim-masked\r\n    \u4e0d\u4ece\u5e8f\u5217\u672b\u7aef\u53bb\u9664\u4f4e\u8d28\u91cf\u78b1\u57fa\u3002\r\n-q | --trim-quality=N\r\n    \u4ece\u5e8f\u5217\u5c3e\u7aef\u53bb\u9664\u78b1\u57fa\u8d28\u91cf\u4f4e\u4e8e\u6b64\u503c\u7684\u78b1\u57fa\u3002\r\n--standard-quality\r\n    \u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u4e3a phred33 \uff0c\u8fd9\u662f\u9ed8\u8ba4\u9009\u9879\u3002\r\n--illumina-quality\r\n    \u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u4e3a phred64 \u3002\r\n-o | --out=FILE\r\n    \u8f93\u51fa\u7684 contigs \u6587\u4ef6\u7684\u6587\u4ef6\u540d\u3002\r\n-k | --kmer=N\r\n    k-mer \u957f\u5ea6\u3002\r\n-t | --trim-length=N\r\n    maximum length of dangling edges to trim\r\n-c | --coverage=FLOAT\r\n    \u53bb\u9664 k-mer \u8986\u76d6\u8bfb\u4f4e\u4e8e\u6b64\u503c\u7684 contigs \u3002\r\n-b | --bubbles=N\r\n    pop bubbles shorter than N bp [3*k]\r\n-b0 | --no-bubbles\r\n    do not pop bubbles\r\n<\/pre>\n<h2>2.1 \u4f7f\u7528 abyss-pe \u5c06 short reads \u7ec4\u88c5\u6210 scaffolds<\/h2>\n<p>\u4f7f\u7528\u5982\u4e0b\u547d\u4ee4\u67e5\u9605 ABYSS \u547d\u4ee4\u7684\u8bf4\u660e\uff1a<\/p>\n<pre>\r\n$ abyss-pe --help\r\n\u6216\u8005\r\n$ less \/opt\/biosoft\/abyss-1.3.7\/share\/man\/man1\/abyss-pe.1\r\n<\/pre>\n<p>\u51e0\u79cd\u4f7f\u7528\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n1 \u4e2a paired-end \u6587\u5e93\uff1a\r\n$ abyss-pe k=64 name=ecoli in='reads1.fa reads2.fa'\r\n\r\n\u591a\u4e2a paired-end \u6587\u5e93\uff1a\r\n$ abyss-pe k=64 name=ecoli lib='lib1 lib2' lib1='lib1_1.fa lib1_2.fa' lib2='lib2_1.fa lib2_2.fa' se='se1.fa se2.fa'\r\n\r\npaired-end \u548c mate-pair \u6587\u5e93\uff1a\r\n$ abyss-pe k=64 name=ecoli lib='pe1 pe2' mp='mp1 mp2' pe1='pe1_1.fa pe1_2.fa' pe2='pe2_1.fa pe2_2.fa' mp1='mp1_1.fa mp1_2.fa' mp2='mp2_1.fa mp2_2.fa' se='se1.fa se2.fa'\r\n\r\n\u4f7f\u7528 RNA-Seq \u7684\u7ec4\u88c5\u7ed3\u679c\u8fdb\u884c rescaffolding \uff1a\r\n$ abyss-pe k=64 name=ecoli lib=pe1 mp=mp1 long=long1 pe1='pe1_1.fa pe1_2.fa' mp1='mp1_1.fa mp1_2.fa' long1=long1.fa\r\n\r\n\u4f7f\u7528 MPI \uff1a\r\nabyss-pe np=8 k=64 name=ecoli in='reads1.fa reads2.fa'\r\n\r\n\u4f7f\u7528\u96c6\u7fa4\uff1a\r\nqsub -N ecoli -t 64 -pe openmpi 8 abyss-pe n=10 in='reads1.fa reads2.fa'\r\n<\/pre>\n<p>\u4f7f\u7528\u591a\u4e2a k \u503c\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u518d\u5bfb\u627e\u6700\u4f73 k \u503c\uff1a<\/p>\n<pre>\r\n$ export k\r\n$ for k in {20..40}; do\r\n$    mkdir k$k\r\n$    abyss-pe -C k$k name=ecoli in=..\/reads.fa\r\n$ done\r\n$ abyss-fac k*\/ecoli-contigs.fa\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. ABySS\u7684\u5b89\u88c5 \u5b89\u88c5google-sparsehash $ sudo r &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2109\">\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\/2109"}],"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=2109"}],"version-history":[{"count":2,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2109\/revisions"}],"predecessor-version":[{"id":2111,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2109\/revisions\/2111"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2109"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2109"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2109"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}