{"id":3610,"date":"2021-11-15T10:54:07","date_gmt":"2021-11-15T02:54:07","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=3610"},"modified":"2021-11-15T10:54:07","modified_gmt":"2021-11-15T02:54:07","slug":"%e4%bd%bf%e7%94%a8pandaseq%e8%bf%9e%e6%8e%a5%e9%87%8d%e5%8f%a0%e7%9a%84paired-end-illumina%e6%95%b0%e6%8d%ae","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=3610","title":{"rendered":"\u4f7f\u7528PANDAseq\u8fde\u63a5\u91cd\u53e0\u7684Paired-End Illumina\u6570\u636e"},"content":{"rendered":"\n<p>PANDAseq\uff08https:\/\/github.com\/neufeld\/pandaseq\uff09\u7528\u4e8e\u5c06Paired-End\u6d4b\u5e8f\u4e14\u6709\u91cd\u53e0\u7684\u53cc\u672b\u7aefreads\u8fde\u63a5\u6210\u4e00\u6761\u8f83\u957f\u7684read\u3002\u8be5\u8f6f\u4ef62021\u5e74\u53d1\u8868\u4e8eBMC Bioinformatics\uff0c\u5e76\u57282017\u5e743\u6708\u66f4\u65b0\u52302.11\u7248\u672c\u3002PANDseq\u8f6f\u4ef6\u5148\u68c0\u6d4b\u53cc\u7aefreads\u91cd\u53e0\u518d\u8fde\u63a5\uff0c\u4f7f\u7528\u65f6\u9ed8\u8ba4\u4f7f\u7528simple_bayesian\u7b97\u6cd5\uff0c\u4e5f\u8fd8\u53ef\u4ee5\u9009\u62e9FastqJoin in\u00a0<a href=\"https:\/\/code.google.com\/p\/ea-utils\/wiki\/FastqJoin\">ea-utils<\/a>, <a href=\"http:\/\/ccb.jhu.edu\/software\/FLASH\/\">FLASH (Fast Length Adjustment of SHort reads)<\/a>\u6216<a href=\"http:\/\/www.exelixis-lab.org\/pear\">PEAR (Paired-End AssembleR)<\/a>\u7b97\u6cd5\u3002\u6b64\u5916\uff0cPANDAseq\u5c06\u53cc\u672b\u7aef\u6570\u636e\u8fde\u63a5\u65f6\uff0c\u80fd\u6839\u636e\u91cd\u53e0\u7ed3\u679c\uff0c\u4fee\u6b63\u4e0d\u5339\u914d\u78b1\u57fa\uff08\u9009\u62e9\u78b1\u57fa\u8d28\u91cf\u9ad8\u7684\u78b1\u57fa\uff09\u548c\u672a\u77e5\u78b1\u57fa\u3002<\/p>\n\n\n\n<h2>1. \u8f6f\u4ef6\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h2>\n\n\n\n<pre class=\"wp-block-code\"><code>wget https:\/\/github.com\/neufeld\/pandaseq\/archive\/refs\/tags\/v2.11.tar.gz -O pandaseq-2.11.tar.gz\ntar zxf pandaseq-2.11.tar.gz\ncd pandaseq-2.11\/\n.\/autogen.sh\n.\/configure --prefix=\/opt\/biosoft\/pandaseq-2.11\nmake -j 4 &amp;&amp; make install \ncd .. &amp;&amp; rm -rf pandaseq-2.11\necho 'PATH=$PATH:\/opt\/biosoft\/pandaseq-2.11\/bin\/' >> ~\/.bashrc\nsource ~\/.bashrc<\/code><\/pre>\n\n\n\n<h2>2. \u8f6f\u4ef6\u7684<a href=\"https:\/\/storage.googleapis.com\/pandaseq\/pandaseq.html\">\u4f7f\u7528<\/a><\/h2>\n\n\n\n<p>\u5e38\u7528\u793a\u4f8b\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>pandaseq -f illumina.1.fastq -r illumina.2.fastq -k 5 -o 5 -F  > out.fastq 2> out.tab<\/code><\/pre>\n\n\n\n<p>\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>-6    default: None\n\t\u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u8868\u793a\u8f93\u5165\u6570\u636e\u662fPhred64\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u3002\u7a0b\u5e8f\u9ed8\u8ba4\u8bc6\u522bPhred33\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u3002\n-A &lt;string>    default: simple_bayesian\n\t\u8bbe\u7f6e\u8f6f\u4ef6\u7684\u7b97\u6cd5\u3002simple_bayesian&#91;:error_estimation]\uff0c\u9ed8\u8ba4\u4f7f\u7528PANDAseq\u8f6f\u4ef6\u53d1\u8868\u6587\u7ae0\u4e2d\u7684\u7b97\u6cd5\uff0c\u53ef\u4ee5\u8f93\u5165\u9519\u8bef\u7387\uff1bea_util\uff0c\u4f7f\u7528FastqJoin\u7b97\u6cd5\uff1bflash\uff0c\u4f7f\u7528FLASH\u7b97\u6cd5\uff1bpear&#91;:random_base]\uff0c\u4f7f\u7528PEAR\u7b97\u6cd5\uff0c\u53ef\u4ee5\u8f93\u5165\u4e00\u4e2a\u968f\u673a\u78b1\u57fa\u7684\u6982\u7387\uff1brdp_mle\uff0c\u4f7f\u7528RDP\u7b97\u6cd5\uff1bstitch\uff0c\u4f7f\u7528Sitch\u7b97\u6cd5\uff1buparse&#91;:error_estimation]\uff0c\u4f7f\u7528UPARSE\/USEARCH\u7b97\u6cd5\uff0c\u53ef\u4ee5\u8f93\u5165\u9519\u8bef\u7387\u3002\n-f &lt;string>    default: None\n\t\u8f93\u5165reads1\u7684FASTQ\u6587\u4ef6\uff0c\u652f\u6301gzip\u6216bzip2\u683c\u5f0f\u7684\u6587\u4ef6\u3002\n-r &lt;string>    default: None\n\t\u8f93\u5165reads2\u7684FASTQ\u6587\u4ef6\uff0c\u652f\u6301gzip\u6216bzip2\u683c\u5f0f\u7684\u6587\u4ef6\u3002\n-F    default: None\n\t\u7a0b\u5e8f\u9ed8\u8ba4\u8f93\u51faFASTA\u7684\u7ed3\u679c\u3002\u82e5\u6dfb\u52a0\u8be5\u53c2\u6570\u5219\u8f93\u51faPhred33\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u7684FASTQ\u683c\u5f0f\u6587\u4ef6\u3002\u5373\u4f7f\u8f93\u5165\u7684FASTQ\u6587\u4ef6\u662fPhred64\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\uff0c\u4e5f\u8f93\u51faPhred33\u683c\u5f0f\u7684\u7ed3\u679c\uff1b\u91cd\u53e0\u533a\u57df\u8f93\u51fa\u4e24\u6761reads\u7684\u5e73\u5747\u78b1\u57fa\u8d28\u91cf\uff0c\u975e\u91cd\u53e0\u533a\u57df\u8f93\u51fa\u5404\u81ea\u539f\u672c\u7684\u78b1\u57fa\u8d28\u91cf\u3002\n-k &lt;int>    default: 2\n\t\u8bbe\u7f6ek-mer\u5e8f\u5217\u8bb0\u5f55\u7684\u4f4d\u7f6e\u4e2a\u6570\u3002\u7a0b\u5e8f\u901a\u8fc7k-mer\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\uff0c\u8bb0\u5f55k-mer\u5e8f\u5217\u51fa\u73b0\u5728reads\u5e8f\u5217\u7684\u4f4d\u7f6e\u4fe1\u606f\u3002\u82e5reads\u6709\u91cd\u590d\uff0c\u5219k-mer\u53ef\u80fd\u51fa\u73b0\u5728\u4e00\u6761read\u7684\u591a\u4e2a\u5730\u65b9\uff0c\u7a0b\u5e8f\u9ed8\u8ba4\u4ec5\u8bb0\u5f552\u4e2a\u4f4d\u7f6e\u4fe1\u606f\u3002\u8be5\u53c2\u6570\u8bbe\u7f6e\u4e0d\u80fd\u8d85\u8fc710\uff0c\u8be5\u503c\u8d8a\u5927\u8d8a\u6d88\u8017\u5185\u5b58\u548c\u8ba1\u7b97\uff0c\u4f46\u662f\u5e94\u8be5\u7ed3\u679c\u4e5f\u66f4\u51c6\u786e\u3002\u6700\u597d\u63a8\u8350\u63d0\u9ad8\u8be5\u503c\uff0c\u76f4\u5230FML\u7684\u9519\u8bef\u63d0\u793a\u53d8\u5c11\u3002\n-o &lt;int>    default: 1\n\t\u8bbe\u7f6e\u9996\u5c3ereads\u6700\u5c0f\u7684\u91cd\u53e0\u78b1\u57fa\u957f\u5ea6\u3002\u4f5c\u8005\u5728\u8f6f\u4ef6\u8bf4\u660e\u4e2d\u8868\u793a\uff1a\u9ed8\u8ba4\u6700\u5c11\u67091\u4e2a\u78b1\u57fa\u91cd\u53e0\uff0c\u4f46\u540e\u7eed\u56de\u6839\u636e\u6253\u5206\u80fd\u53bb\u9664\u91cd\u53e0\u8f83\u5c11\u7684\u7ed3\u679c\u3002\u5b9e\u9645\u6d4b\u8bd5\u7ed3\u679c\u4e2d\u5219\u4fdd\u7559\u6700\u5c11\u67093\u4e2a\u78b1\u57fa\u91cd\u53e0\u7684\u6570\u636e\u3002\u4e2a\u4eba\u63a8\u8350\u6839\u636e\u6570\u636e\u7684\u5e73\u5747\u91cd\u53e0\u957f\u5ea6\u8bbe\u7f6e\u4e3a5\u6216\u66f4\u9ad8\u3002\n-O &lt;int>    default: read length\n\t\u8bbe\u7f6e\u9996\u5c3ereads\u6700\u957f\u7684\u91cd\u53e0\u78b1\u57fa\u957f\u5ea6\u3002\n-t &lt;float>    default: 0.6\n\t\u8bbe\u7f6e\u6700\u4f4e\u5f97\u5206\u9608\u503c\uff0c\u8be5\u53c2\u6570\u503c\u57280~1\u4e4b\u95f4\u3002\u5177\u4f53\u7684\u8ba1\u5206\u65b9\u6cd5\u8f6f\u4ef6\u8bf4\u660e\u4e66\u4e2d\u6ca1\u6709\u3002\n-T &lt;int>    default: max\n\t\u8bbe\u7f6e\u7ebf\u7a0b\u6570\uff0c\u9ed8\u8ba4\u4e3a\u8ba1\u7b97\u673a\u7684\u6700\u5927CPU\u7ebf\u7a0b\u6570\u3002\u82e5\u7f16\u8bd1PANDAseq\u8f6f\u4ef6\u65f6\u4f7f\u7528\u4e86pthreads\uff0c\u5219\u652f\u6301\u8be5\u53c2\u6570\u8bbe\u7f6e\u66f4\u5927\u7684\u503c\u3002\u7531\u4e8e\u8ba1\u7b97\u901f\u5ea6\u53ef\u80fd\u53d7\u5230I\/O\u74f6\u9888\uff0c\u5373\u4f7f\u8bbe\u7f6e\u4e86\u5f88\u9ad8\u7684\u53c2\u6570\u503c\uff0c\u771f\u5b9e\u53ef\u80fd\u4ec5\u80fd\u5229\u75288~16\u4e2aCPU\u7ebf\u7a0b\u3002\n-l &lt;int>    default: None\n\t\u8bbe\u7f6e\u6700\u77ed\u5e8f\u5217\u957f\u5ea6\u3002\u53bb\u9664\u8fde\u63a5\u540e\u957f\u5ea6\u4f4e\u4e8e\u8be5\u503c\u7684\u5e8f\u5217\uff0c\u9ed8\u8ba4\u4fdd\u7559\u6240\u6709\u5e8f\u5217\u3002\n-L &lt;int>    default: None\n\t\u8bbe\u7f6e\u6700\u957f\u5e8f\u5217\u957f\u5ea6\u3002\u53bb\u9664\u8fde\u63a5\u540e\u957f\u5ea6\u9ad8\u4e8e\u8be5\u503c\u7684\u5e8f\u5217\uff0c\u9ed8\u8ba4\u4fdd\u7559\u6240\u6709\u5e8f\u5217\u3002\n-N    default: None\n\u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u5219\u8868\u793a\u53bb\u9664\u8fde\u63a5\u540e\u542b\u6709\u78b1\u57faN\u7684\u5e8f\u5217\u3002<\/code><\/pre>\n\n\n\n<p>\u7a0b\u5e8f\u9ed8\u8ba4\u5728\u6807\u51c6\u8f93\u51fa\u4e2d\u7ed9\u51faFASTA\u6216FASTQ\u7684\u7ed3\u679c\u6570\u636e\uff0c\u5728\u6807\u51c6\u9519\u8bef\u8f93\u51fa\u4e2d\u7ed9\u51fa\u5404reads\u5bf9\u7684\u91cd\u53e0\u4fe1\u606f\u548c\u7edf\u8ba1\u4fe1\u606f\u3002<\/p>\n\n\n\n<p>\u7edf\u8ba1\u4fe1\u606f\u663e\u793a\u6bcf\u4e2a\u8ba1\u7b97\u7684CPU\u7ebf\u7a0b\u7ed3\u679c\uff0c\u82e5\u4ec5\u75281\u4e2aCPU\u7ebf\u7a0b\uff0c\u5219\u80fd\u76f4\u63a5\u770b\u5230\u6240\u6709\u6570\u636e\u7684\u7edf\u8ba1\u7ed3\u679c\uff0c\u793a\u4f8b\u5982\u4e0b\uff0c\u53ef\u4ee5\u770b\u5230\u6d88\u8017\u7684\u65f6\u95f4(ELAPSED)\u3001\u91cd\u53e0\u78b1\u57fa\u957f\u5ea6\u53ca\u6570\u91cf(OVERLAPS\uff0c\u6309\u987a\u5e8f\u8868\u793a\u91cd\u53e0\u957f\u5ea6\u4e3a1,2,3\u2026bp\u7684reads\u5bf9\u4e2a\u6570)\u548c\u5404reads\u5bf9\u6570\u91cf\uff1a\u8f93\u5165(READS)\u3001\u672a\u80fd\u627e\u5230\u91cd\u53e0(NOALGN)\u3001\u91cd\u53e0\u5f97\u5206\u4f4e(LOWQ)\u3001\u591a\u957f\u6216\u8fc7\u77ed(BADR)\u3001\u8ba1\u7b97\u8f83\u8d39\u65f6(SLOW)\u548c\u8f93\u51fa(OK)\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>0x1471a80:0     STAT    TIME    Mon Nov 15 09:40:09 2021\n0x1471a80:0     STAT    ELAPSED 277\n0x1471a80:0     STAT    READS   10220063\n0x1471a80:0     STAT    NOALGN  455052\n0x1471a80:0     STAT    LOWQ    754593\n0x1471a80:0     STAT    BADR    0\n0x1471a80:0     STAT    SLOW    2077539\n0x1471a80:0     STAT    OK      9010418\n0x1471a80:0     STAT    OVERLAPS        0 0 0 0 0 143771 155071 166920 167346 211873 218965 219605 224772 224272 229920 231389 232102 \u2026<\/code><\/pre>\n\n\n\n<p>\u5e38\u89c1reads\u7684\u91cd\u53e0\u4fe1\u606f\u4e2d\u7b2c\u4e09\u5217\uff1a<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table><tbody><tr><td>INFO&nbsp;&nbsp;&nbsp; BESTOLP<\/td><td>\u6700\u4f18\u91cd\u53e0\u53c2\u6570\u3002<\/td><\/tr><tr><td>ERR&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; LOWQ<\/td><td>\u5f97\u5206\u4f4e\u8bbe\u5b9a\u7684\u6700\u4f4e\u9608\u503c\u3002<\/td><\/tr><tr><td>DBG&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; FML<\/td><td>k-mer\u51fa\u73b0\u5728read\u4e2d\u7684\u6b21\u6570\u8d85\u8fc7\u4e86\u6307\u5b9a\u7684\u9608\u503c\uff0c\u8868\u793a\u627e\u7684\u91cd\u53e0\u53ef\u80fd\u4e0d\u51c6\u786e\u3002<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>PANDAseq\uff08https:\/\/github.com\/neufeld\/pand &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=3610\">\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\/3610"}],"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=3610"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/3610\/revisions"}],"predecessor-version":[{"id":3612,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/3610\/revisions\/3612"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3610"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=3610"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=3610"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}