{"id":816,"date":"2021-12-11T08:52:06","date_gmt":"2021-12-11T00:52:06","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=816"},"modified":"2022-07-28T23:19:35","modified_gmt":"2022-07-28T15:19:35","slug":"srst2%e4%bd%bf%e7%94%a8%e7%9f%ad%e5%ba%8f%e5%88%97%e9%89%b4%e5%ae%9amlst%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=816","title":{"rendered":"SRST2:\u4f7f\u7528\u77ed\u5e8f\u5217\u9274\u5b9aMLST\u5206\u578b"},"content":{"rendered":"<p>\u5b89\u88c5\uff1a<\/p>\n<pre>#\u901a\u8fc7conda\u5b89\u88c5\nconda create -n srst2 srst2\nconda activate srst2\n#\u901a\u8fc7pip\u5b89\u88c5\npip install srst2\n<\/pre>\n<p>\u4e0b\u8f7dMLST\u6570\u636e\u5e93<\/p>\n<pre>getmlst.py --species \"Streptococcus agalactiae\"\n<\/pre>\n<p>\u4f7f\u7528<\/p>\n<pre>srst2 --input_pe S1_1.fastq.gz S1_2.fastq.gz --output S1 --log --mlst_db Streptococcus_agalactiae.fasta --mlst_definitions profiles_csv --mlst_delimiter _\n##\u53cc\u672b\u7aef\u6d4b\u5e8f\u6587\u4ef6\u547d\u540d_1\u548c_2\n<\/pre>\n<p>MLST\u626b\u63cf\u7ed3\u679c\u5b57\u6bb5\uff1a<\/p>\n<p>Sample\uff1a\u626b\u63cf\u6570\u636e\u7684\u6837\u54c1\u540d\u79f0\uff0c\u6bd4\u5982S1\uff0c\u6216\u8005SRR1002045\u7b49<br \/>\nST\uff1a\u626b\u63cf\u6bd4\u5bf9\u6570\u636e\u5e93\u540e\u83b7\u5f97ST\u578b\u522b<br \/>\n7\u4e2a\u5177\u4f53\u7ba1\u5bb6\u57fa\u56e0\uff1a\u626b\u63cf\u6bcf\u4e2a\u57fa\u56e0allele\u5206\u914d\u7684\u578b\u522b<br \/>\nmismatches\uff1a7\u4e2a\u7ba1\u5bb6\u57fa\u56e0\u4e2d\u662f\u5426\u6709\u4e0d\u5339\u914d\u7684\u78b1\u57fa<br \/>\nuncertainty\uff1a\u7531\u4e8e\u5e8f\u5217\u6df1\u5ea6\u6216\u8005\u8986\u76d6\u5ea6\u4e0d\u591f\u9020\u6210\u7684\u4e0d\u786e\u5b9a\u60c5\u51b5<br \/>\ndepth\uff1a\u57fa\u56e0\u6bd4\u5bf9\u7684\u8986\u76d6\u5ea6<br \/>\nmaxMAF\uff1a\u626b\u63cf\u76847\u4e2a\u7ba1\u5bb6\u57fa\u56e0\u4e2d\u6700\u9ad8\u7684minor\u7b49\u4f4d\u57fa\u56e0\u9891\u7387<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5b89\u88c5\uff1a #\u901a\u8fc7conda\u5b89\u88c5 conda create -n srst2 srst2 conda activate srst2 #\u901a\u8fc7pip\u5b89\u88c5 pip install srst2 \u4e0b\u8f7dMLST\u6570\u636e\u5e93 getmlst.py &#8211;species &#8220;Streptococcus agalactiae&#8221; \u4f7f\u7528 srst2 &#8211;input_pe S1_1.fastq.gz S1_2.fastq.gz &#8211;output S1 &#8211;log &#8211;mlst_db Streptococcus_agalactiae.fasta &#8211;mlst_definitions profiles_csv &#8211;mlst_delimiter _ ##\u53cc\u672b\u7aef\u6d4b\u5e8f\u6587\u4ef6\u547d\u540d_1\u548c_2 MLST\u626b\u63cf\u7ed3\u679c\u5b57\u6bb5\uff1a Sample\uff1a\u626b\u63cf\u6570\u636e\u7684\u6837\u54c1\u540d\u79f0\uff0c\u6bd4\u5982S1\uff0c\u6216\u8005SRR1002045\u7b49 ST\uff1a\u626b\u63cf\u6bd4\u5bf9\u6570\u636e\u5e93\u540e\u83b7\u5f97ST\u578b\u522b 7\u4e2a\u5177\u4f53\u7ba1\u5bb6\u57fa\u56e0\uff1a\u626b\u63cf\u6bcf\u4e2a\u57fa\u56e0allele\u5206\u914d\u7684\u578b\u522b mismatches\uff1a7\u4e2a\u7ba1\u5bb6\u57fa\u56e0\u4e2d\u662f\u5426\u6709\u4e0d\u5339\u914d\u7684\u78b1\u57fa uncertainty\uff1a\u7531\u4e8e\u5e8f\u5217\u6df1\u5ea6\u6216\u8005\u8986\u76d6\u5ea6\u4e0d\u591f\u9020\u6210\u7684\u4e0d\u786e\u5b9a\u60c5\u51b5 depth\uff1a\u57fa\u56e0\u6bd4\u5bf9\u7684\u8986\u76d6\u5ea6 maxMAF\uff1a\u626b\u63cf\u76847\u4e2a\u7ba1\u5bb6\u57fa\u56e0\u4e2d\u6700\u9ad8\u7684minor\u7b49\u4f4d\u57fa\u56e0\u9891\u7387<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/816"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=816"}],"version-history":[{"count":4,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/816\/revisions"}],"predecessor-version":[{"id":864,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/816\/revisions\/864"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=816"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=816"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=816"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}