{"id":2122,"date":"2014-06-09T21:41:31","date_gmt":"2014-06-09T13:41:31","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2122"},"modified":"2014-06-09T21:41:31","modified_gmt":"2014-06-09T13:41:31","slug":"%e4%bd%bf%e7%94%a8-musket-%e8%bf%9b%e8%a1%8c-reads-correction","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2122","title":{"rendered":"\u4f7f\u7528 musket \u8fdb\u884c reads correction"},"content":{"rendered":"<h1>1. musket \u7b80\u4ecb<\/h1>\n<p>Musket is a an efficient multistage k-mer spectrum based corrector for illumina short read data\u3002<br \/>\n\u5176\u53d1\u8868\u6587\u732e\u4e3a\uff1a<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/29\/3\/308.full\" target=\"_blank\">Liu Y, Schr\u00f6der J, Schmidt B. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data[J]. Bioinformatics, 2013, 29(3): 308-315.<\/a><br \/>\n\u8be5\u8f6f\u4ef6\u4f7f\u7528\u7b80\u5355\uff0c\u80fd\u8fdb\u884c\u591a\u7ebf\u7a0b\u8fd0\u884c\uff0c\u901f\u5ea6\u5feb\u3002<\/p>\n<h1>2. musket \u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/cznic.dl.sourceforge.net\/project\/musket\/musket-1.1.tar.bz\r\n$ tar zxf musket-1.1.tar.bz -C \/opt\/biosoft\r\n$ cd \/opt\/biosoft\/musket-1.1\/\r\n$ make\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/musket-1.1\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<p>\u5728\u8f6f\u4ef6\u7f16\u8bd1\u524d\uff0c\u53ef\u4ee5\u4fee\u6539 Makefile \u4e2d\u7b2c\u4e8c\u884c\u5185\u5bb9 \u201cMACROS = -DMAX_SEQ_LENGTH=200 -DMAX_KMER_SIZE=28\u201d\u3002\u6b64\u884c\u8868\u793a\uff0c\u8f6f\u4ef6\u5141\u8bb8\u7684\u6700\u5927 read \u957f\u5ea6\u4e3a 200\uff0c \u6700\u5927\u7684 kmer \u4e3a 28\u3002\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u9700\u6c42\u4fee\u6539\u6b64\u503c\u3002<\/p>\n<h1>3. musket \u53c2\u6570<\/h1>\n<pre>\r\n-k int unit\r\n\u6b64\u53c2\u6570\u540e\u6709 2 \u4e2a\u503c\uff0c\u524d\u8005\u4e3a k-mer \u7684\u5927\u5c0f\uff0c\u9ed8\u8ba4\u503c\u4e3a 21\u3002\u540e\u8005\u662f distinct k-mers \u7684\u6570\u76ee\uff0c\u5982\u679c\u662f\u5168\u57fa\u56e0\u7ec4\u6d4b\u5e8f\u7684\u6570\u636e\uff0c\u5219\u53ef\u4ee5\u7406\u89e3\u4e3a\u57fa\u56e0\u7ec4\u7684\u5927\u5c0f\u3002\u5f53\u7136\uff0c\u7531\u4e8e read \u4e2d\u53ef\u80fd\u5b58\u5728\u9519\u8bef\uff0c\u56e0\u6b64 distinct k-mers \u7684\u6570\u76ee\u6bd4\u57fa\u56e0\u7ec4\u8981\u5927\u3002\u5982\u679c\u5185\u5b58\u591f\u7528\uff0c\u5219\u6211\u4e2a\u4eba\u63a8\u8350\u8bbe\u7f6e\u4e3a\u57fa\u56e0\u7ec4\u5927\u5c0f\u7684 2 \u500d\u3002\u8be5\u503c\u7684\u8bbe\u7f6e\u4e3b\u8981\u7528\u4e8e\u5e73\u8861\u5185\u5b58\u7684\u6d88\u8017\uff0c\u5bf9\u7ed3\u679c\u65e0\u5f71\u54cd\u3002\r\n-o str\r\n\u6b64\u53c2\u6570\u8bbe\u7f6e\u51fa\u5904\u6587\u4ef6\u7684\u6587\u4ef6\u540d\u3002\u8bbe\u7f6e\u6b64\u53c2\u6570\u540e\uff0c\u5219\u4e0d\u7ba1\u8f93\u5165\u6587\u4ef6\u6709\u591a\u5c11\uff0c\u53ea\u4f1a\u8f93\u51fa\u4e00\u4e2a\u6587\u4ef6\u3002\u6b64\u53c2\u6570\u548c\u4e0b\u4e00\u4e2a\u53c2\u6570 \"-omulti\" \u662f\u4e92\u65a5\u7684\uff0c\u4ec5\u80fd\u8bbe\u7f6e\u5176\u4e2d\u4e00\u4e2a\u3002\r\n-omulti str\r\n\u6b64\u53c2\u6570\u8bbe\u7f6e\u51fa\u5904\u6587\u4ef6\u7684\u6587\u4ef6\u540d\u3002\u8bbe\u7f6e\u6b64\u53c2\u6570\u540e\uff0c\u6bcf\u4e2a\u8f93\u5165\u6587\u4ef6\u90fd\u4f1a\u5bf9\u5e94\u4e00\u4e2a\u8f93\u51fa\u6587\u4ef6\u3002\r\n-p int\r\n\u7a0b\u5e8f\u80fd\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\u3002\u9ed8\u8ba4\u503c\u4e3a 2\u3002\u8be5\u503c\u8981\u8bbe\u7f6e\u4e3a >= 2\u3002\r\n-zlib int\r\n\u8bbe\u7f6e\u8f93\u51fa\u7684\u6587\u4ef6\u662f\u5426\u538b\u7f29\uff0c\u9ed8\u8ba4\u503c\u4e3a 0\uff0c \u5373\u4e0d\u538b\u7f29\u3002\r\n-maxtrim int\r\n\u5141\u8bb8 trim \u6389\u7684\u6700\u5927\u78b1\u57fa\u6570\u3002\u8be5\u53c2\u6570\u9ed8\u8ba4\u503c\u4e3a 0\uff0c \u5373\u8868\u793a\u4e0d\u8fdb\u884c trim\u3002\u82e5\u6b64\u53c2\u6570\u4e0d\u4e3a 0\uff0c \u5219\u7a0b\u5e8f\u5728\u5bf9\u4e00\u4e2a read \u8fdb\u884c error correction \u540e\uff0c\u518d\u5bf9\u8be5 read \u8fdb\u884c trim\u3002trim \u7684\u65b9\u6cd5\u4e3a\uff1a\u7a0b\u5e8f\u5bfb\u627e\u6b64 read \u4e2d\u6ca1\u6709\u9519\u8bef\u78b1\u57fa\u7684\u5b50\u5e8f\u5217\uff0c\u7136\u540e\u53d6\u51fa\u6700\u957f\u7684\u5b50\u5e8f\u5217\uff0c\u82e5\u6700\u957f\u5b50\u5e8f\u5217\u957f\u5ea6\u6ee1\u8db3\u6b64\u53c2\u6570\u7684\u8bbe\u5b9a\uff0c\u5219\u8fdb\u884c trim\uff0c\u82e5\u4e0d\u6ee1\u8db3\u53c2\u6570\u8bbe\u5b9a\uff0c\u5219\u4e0d\u8fdb\u884c trim\u3002\r\n-inorder\r\n\u6b64\u53c2\u6570\u662f\u8f93\u51fa\u6587\u4ef6\u7684 reads \u987a\u5e8f\u548c\u8f93\u5165\u6587\u4ef6\u4e00\u81f4\u3002\u5728\u8fdb\u884c paired reads \u7684\u4fee\u6b63\u65f6\uff0c\u4e00\u5b9a\u8981\u52a0\u4e0a\u8be5\u53c2\u6570\u3002\r\n-lowercase\r\n\u662f\u8f93\u51fa\u6587\u4ef6\u4e2d\u7684\u88ab\u4fee\u6b63\u7684\u78b1\u57fa\u4e3a\u5c0f\u5199\u5b57\u6bcd\u3002\u9ed8\u8ba4\u503c\u4e3a 0 \u3002\r\n-multik bool\r\n\u8bbe\u7f6e\u662f\u5426\u53ef\u4ee5\u4f7f\u7528\u591a\u4e2a k-mer sizes \u6765\u8fdb\u884c error correction\u3002\u9ed8\u8ba4\u503c\u4e3a 0\u3002\u5f53\u8bbe\u7f6e\u4e3a 1 \u65f6\uff0c \u5219\u53ef\u4ee5\u8bbe\u7f6e\u591a\u4e2a k-mer \u503c\uff0c\u5982 \"-k 21 536870912 -k 23 268435456\"\u3002\r\n<\/pre>\n<h1>4. \u5e38\u7528\u7684\u4e00\u4e9b\u4f8b\u5b50<\/h1>\n<pre>\r\n$ musket -k 21 536870912 -p 12 reads.fa reads2.fa -o output.fa\r\n$ musket -p 12 reads.fa reads2.fa -o output.fa\r\n$ musket reads.fa reads2.fa -o output.fa -inorder\r\n\r\n$ musket lib1_reads1.fastq lib1_reads2.fastq lib2_reads1.fastq lib2_reads2.fastq -omulti output -inorder\r\n\u4e0a\u8ff0\u547d\u4ee4\u751f\u6210 4 \u4e2a\u6587\u4ef6 output.0 output.1 output.2 output.3 \u6309\u987a\u5e8f\u5206\u522b\u5bf9\u5e94\u524d 4 \u4e2a\u8f93\u5165\u6587\u4ef6\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. musket \u7b80\u4ecb Musket is a an efficient mu &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2122\">\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\/2122"}],"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=2122"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2122\/revisions"}],"predecessor-version":[{"id":2123,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2122\/revisions\/2123"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2122"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2122"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2122"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}