{"id":61790,"date":"2024-11-19T16:47:07","date_gmt":"2024-11-19T08:47:07","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61790"},"modified":"2024-11-19T16:47:07","modified_gmt":"2024-11-19T08:47:07","slug":"%e5%bc%af%e9%81%93%e5%bf%ab%e6%89%8d%e6%98%af%e7%9c%9f%e7%9a%84%e5%bf%ab%ef%bc%81%e8%bf%99%e6%ac%be%e5%9f%ba%e4%ba%8e%e5%90%8e%e7%bc%80%e6%a0%91%e7%ae%97%e6%b3%95","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61790","title":{"rendered":"\u201c\u5f2f\u9053\u201d\u5feb\u624d\u662f\u771f\u7684\u5feb\uff01\u8fd9\u6b3e\u57fa\u4e8e\u201c\u540e\u7f00\u6811\u201d\u7b97\u6cd5\u7684\u57fa\u56e0\u7ec4\u6bd4\u5bf9\u5de5\u5177\uff0c\u7b80\u76f4\u662f\u5171\u7ebf\u6027\u4e0eSNP\u68c0\u6d4b\u795e\u5668\uff01"},"content":{"rendered":"\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005304883_BF563115-F399-4ecf-ADF5-90144063FFD3.png?resize=640%2C142\" alt=\"\" class=\"wp-image-61791\" width=\"640\" height=\"142\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005304883_BF563115-F399-4ecf-ADF5-90144063FFD3.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005304883_BF563115-F399-4ecf-ADF5-90144063FFD3.png?resize=300%2C67 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u55e8\uff0c\u6211\u662f\u5c0f\u5e08\u59b9\uff0c\u5f88\u9ad8\u5174\u80fd\u591f\u548c\u5927\u5bb6\u4e00\u8d77\u6765\u5b66\u4e60\u751f\u7269\u4fe1\u606f\u5b66\u3002\u5982\u679c\u8bf4\u8001\u5e08\u8ba9\u4f60\u53bb\u627e\u4e24\u4e2a\u4e2a\u4f53\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u60c5\u51b5\uff0c\u76f8\u4fe1\u5f88\u591a\u4eba\u90fd\u77e5\u9053\u5148\u9009\u53c2\u8003\u57fa\u56e0\u7ec4\u8fdb\u884cBWA\u6bd4\u5bf9\uff0c\u5f97\u5230bam\u6587\u4ef6\u540e\u4f7f\u7528GATK\u6216samtools\u8f6f\u4ef6\u7b49\u7b49\u4e00\u5957\u6d41\u7a0b\u5f97\u5230VCF\u6587\u4ef6\uff0c\u6700\u540e\u8fdb\u884c\u6ce8\u91ca\u5c31\u5f97\u5230\u57fa\u56e0\u7ec4\u4e4b\u95f4\u7684\u53d8\u5f02\u60c5\u51b5\u4e86\u3002\u4f46\u8fd9\u662f\u6709\u539f\u59cb\u6570\u636e\u7684\u60c5\u51b5\uff0c\u90a3\u5047\u8bbe\u6211\u4eec\u662f\u60f3\u6bd4\u8f83\u4e24\u6761\u57fa\u56e0\u7ec4\u6587\u4ef6\u7684\u5dee\u5f02\u5462\uff1f\u624b\u91cc\u6ca1\u6709raw data\u53c8\u5982\u4f55\u8fdb\u884c\u57fa\u56e0\u7ec4\u53d8\u5f02\u68c0\u6d4b\u5462\uff1f<strong>\u672c\u6b21\u4ecb\u7ecd\u7684\u8f6f\u4ef6\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u5e08\u59b9\u79df\u8d41\u6027\u4ef7\u6bd4\u5c45\u9ad8\u7684\u670d\u52a1\u5668~<\/strong><\/p>\n\n\n\n<p>\u57fa\u56e0\u7ec4\u5171\u7ebf\u6027\u795e\u5668MUMmer4\u8fd9\u5c31\u6765\u5566\uff0cMUMmer\u80fd\u591f\u7528\u4e8e\u7814\u7a76\u7ec6\u83cc\u4e0d\u540c\u83cc\u682a\u95f4\u7684\u57fa\u56e0\u7ec4\u5012\u4f4d\u73b0\u8c61\uff0c\u5206\u6790\u5927\u9f20\u4e0e\u5c0f\u9f20\u57fa\u56e0\u7ec4\u5728\u8fdb\u5316\u8fc7\u7a0b\u4e2d\u7684\u91cd\u6392\uff0c\u4ee5\u53ca\u6bd4\u8f83\u540c\u4e00\u7269\u79cd\u4e0d\u540c\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7248\u672c\u7684\u5dee\u5f02\u7b49\u3002\u5176\u57fa\u4e8e\u540e\u7f00\u6811\u7b97\u6cd5\uff0c\u5176\u8fd0\u884c\u901f\u5ea6\u8fdc\u8d85BLASTZ\uff08\u57fa\u4e8ek-mers\uff09\u3002\u540e\u7f00\u6811\uff08Suffix tree\uff09\u662f\u4e00\u79cd\u6570\u636e\u7ed3\u6784\uff0c\u80fd\u5feb\u901f\u89e3\u51b3\u5f88\u591a\u5173\u4e8e\u5b57\u7b26\u4e32\u7684\u95ee\u9898\u3002<\/p>\n\n\n\n<p>MUMmer\u662f\u4e00\u79cd\u5feb\u901f\u6bd4\u5bf9\u5927DNA\u5e8f\u5217\u7684\u7cfb\u7edf\u3002\u5b83\u53ef\u4ee5\u5bf9\u9f50\uff1a<\/p>\n\n\n\n<ul>\n<li>\u5168\u57fa\u56e0\u7ec4\u5230\u5176\u4ed6\u57fa\u56e0\u7ec4<\/li>\n\n\n\n<li>\u5927\u57fa\u56e0\u7ec4\u76f8\u4e92\u7ec4\u88c5<\/li>\n\n\n\n<li>\u90e8\u5206\uff08\u8349\u7a3f\uff09\u57fa\u56e0\u7ec4\u5e8f\u5217\u76f8\u4e92\u8fde\u63a5<\/li>\n\n\n\n<li>\u6216\u8005\uff08\u5728\u7248\u672c4\u4e2d\uff09\u5bf9\u57fa\u56e0\u7ec4\u8fdb\u884c\u4e00\u7ec4\u8bfb\u53d6\u3002<\/li>\n<\/ul>\n\n\n\n<p>\u524d\u51e0\u5929\u5c0f\u5e08\u59b9\u7ed9\u5927\u5bb6\u5e26\u6765\u4e86\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u4e00\u7ad9\u5f0f\u7684\u5206\u4eab\uff01\u4eca\u5929\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u7684\u662f\u4e00\u4e2a\u975e\u5e38\u5f3a\u5927\u57fa\u56e0\u7ec4\u5171\u7ebf\u6027\u795e\u5668\u5de5\u5177\u2014\u2014MUMmer\uff0c\u540c\u65f6\u4e5f\u53ef\u4ee5\u505aSNP\u68c0\u6d4b\u3002<strong>\u9057\u4f20\u5206\u6790\u53ef\u96be\u4e0d\u5012\u751f\u4fe1\u9ad8\u624b\u5c0f\u5e08\u59b9\uff0c\u8981\u662f\u540c\u5b66\u4eec\u6709\u81ea\u5df1\u505a\u4e0d\u4e86\u7684\u751f\u4fe1\u5206\u6790\uff0c\u6b22\u8fce\u968f\u65f6\u8054\u7cfb\u6211\uff01\uff01\uff01<\/strong><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005321620_5E4B9378-52FA-4f3f-A416-405D41E15F83.png?resize=640%2C259\" alt=\"\" class=\"wp-image-61792\" width=\"640\" height=\"259\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005321620_5E4B9378-52FA-4f3f-A416-405D41E15F83.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005321620_5E4B9378-52FA-4f3f-A416-405D41E15F83.png?resize=300%2C121 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p><strong>\u4e00\u3001\u4e0b\u8f7d\u548c\u5b89\u88c5<\/strong><strong><\/strong><\/p>\n\n\n\n<p>mummer\u53d1\u8868\u4e8e1999\u5e74\uff0c\u662f\u7ecf\u5178\u7684\u5168\u5c40\u6bd4\u5bf9\u8f6f\u4ef6\u3002\u4e00\u76f4\u6709\u66f4\u65b0\u7ef4\u62a4\uff0c\u6700\u65b0\u7684\u7248\u672c\u662f2020\u5e7410\u6708\u53d1\u5e03\u76844.0.0 candidate 1\u7248\u672c\uff0c\u4e0b\u9762\u5c31\u7ed9\u5927\u5bb6\u5e26\u6765\u6700\u65b0\u9c9c\u7684mummer4\u5b89\u88c5\u6307\u5357\uff1a<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005646187_8C2DBC46-87B4-45df-A30F-80127FB51694.png?resize=640%2C191\" alt=\"\" class=\"wp-image-61797\" width=\"640\" height=\"191\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005646187_8C2DBC46-87B4-45df-A30F-80127FB51694.png?w=553 553w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005646187_8C2DBC46-87B4-45df-A30F-80127FB51694.png?resize=300%2C90 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u56fe1 Mummer\u5de5\u5177\u5404\u7248\u672c\u66f4\u65b0\u60c5\u51b5<\/p>\n\n\n\n<p>\u9996\u5148\u6211\u4eec\u9700\u8981\u5148\u5b89\u88c5\u6240\u9700\u7684REQUIREMENTS\uff0c\u5efa\u8bae\u65b0\u5efa\u4e00\u4e2aconda\u73af\u5883<\/p>\n\n\n\n<ul>\n<li>perl5 (5.6.0)<\/li>\n\n\n\n<li>sh<\/li>\n\n\n\n<li>sed<\/li>\n\n\n\n<li>awk<\/li>\n<\/ul>\n\n\n\n<p><strong>OPTIONAL UTILITIES<\/strong><strong><\/strong><\/p>\n\n\n\n<ul>\n<li>fig2dev (3.2.3)<\/li>\n\n\n\n<li>gnuplot (4.0)<\/li>\n\n\n\n<li>xfig (3.2)<\/li>\n<\/ul>\n\n\n\n<p>\u63a5\u4e0b\u6765\u662f\u5b89\u88c5\u90e8\u5206\uff1a<\/p>\n\n\n\n<p><strong>$ conda create -n mummer4<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ conda activate mummer4<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ conda install -c conda-forge perl<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ conda install -c conda-forge fig2dev<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ conda install -c conda-forge xfig<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ mkdir mummer4<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ cd mummer4<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ wget <\/strong><strong>https:\/\/github.com\/mummer4\/mummer\/releases\/download\/v4.0.0rc1\/mummer-4.0.0rc1.tar.gz<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ tar -zxvf mummer-4.0.0rc1.tar.gz<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ .\/configure &#8211;prefix=\/path\/to\/installation<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ make<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ make install<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ export PATH=$current_path\/mummer-4.0.0rc1:$PATH <\/strong><strong><\/strong><\/p>\n\n\n\n<p>Mummer\u4e00\u5171\u67094\u4e2a\u5de5\u4f5c\u6d41\u7a0b\uff1a<\/p>\n\n\n\n<ul>\n<li><strong>nucmer<\/strong>: \u7531Perl\u5199\u7684\u6d41\u7a0b\uff0c\u7528\u4e8e\u8054\u914d\u5f88\u76f8\u8fd1(closely related)\u6838\u9178\u5e8f\u5217\u3002\u5b83\u6bd4\u8f83\u9002\u5408\u5b9a\u4f4d\u548c\u5c55\u793a\u9ad8\u5ea6\u4fdd\u5b88\u7684DNA\u5e8f\u5217\u3002\u6ce8\u610f\uff0c\u4e3a\u4e86\u63d0\u9ad8nucmer\u7684\u7cbe\u786e\u6027\uff0c\u6700\u597d\u628a\u8f93\u5165\u5e8f\u5217\u5148\u505a\u906e\u76d6(mask)\u907f\u514d\u4e0d\u611f\u5174\u8da3\u7684\u5e8f\u5217\u7684\u8054\u914d\uff0c\u6216\u8005\u4fee\u6539\u5355\u4e00\u6027\u9650\u5236\u964d\u4f4e\u91cd\u590d\u5bfc\u81f4\u7684\u8054\u914d\u6570\u3002<\/li>\n\n\n\n<li><strong>promer<\/strong>\uff1a\u4e5f\u662fPerl\u5199\u7684\u6d41\u7a0b\uff0c\u5b83\u4ee5\u7ffb\u8bd1\u540e\u7684\u6c28\u57fa\u9178\u5e8f\u5217\u8fdb\u884c\u8054\u914d\uff0c\u5de5\u4f5c\u539f\u7406\u540cnucmer\u3002<\/li>\n\n\n\n<li><strong>run-mummer1,run-mummer3<\/strong>\uff1a\u4e24\u8005\u662f\u57fa\u4e8ecshell\u5199\u7684\u6d41\u7a0b\uff0c\u7528\u4e8e\u4e24\u4e2a\u5e8f\u5217\u7684\u5e38\u89c4\u8054\u914d\uff0c\u548cpromer,nucmer\u7c7b\u4f3c\uff0c\u53ea\u4e0d\u8fc7\u80fd\u591f\u81ea\u52a8\u8bc6\u522b\u5e8f\u5217\u7c7b\u578b\u3002\u5b83\u4eec\u64c5\u957f\u8054\u914d\u76f8\u4f3c\u5ea6\u9ad8\u7684DNA\u5e8f\u5217\uff0c\u627e\u5230\u5b83\u4eec\u7684\u4e0d\u540c\uff0c\u4e5f\u5c31\u662f\u9002\u5408\u627eSNP\u6216\u8005\u7ea0\u9519\u3002\u524d\u8005\u7528\u4e8e1v1\u65e0\u91cd\u6392\uff0c\u540e\u80051v\u591a\u6709\u91cd\u6392<\/li>\n<\/ul>\n\n\n\n<p><strong>\u4e8c\u3001\u5e38\u7528\u547d\u4ee4<\/strong><strong><\/strong><\/p>\n\n\n\n<p>1\u3001\u6bd4\u5bf9<\/p>\n\n\n\n<p>nucmer\u901a\u8fc7\u6bd4\u8f83\u57fa\u56e0\u7ec4\u83b7\u53d6\u7a81\u53d8\u4fe1\u606f\uff0c\u8be5\u65b9\u6cd5\u9002\u5408\u591a\u4e2a\u8fd1\u7f18\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u6bd4\u8f83\uff0c\u53ef\u4ee5\u7528\u4e8e\u591aFasta\u6570\u636e\u6587\u4ef6\u4e2d\u5305\u542b\u7684\u6838\u82f7\u9178\u5e8f\u5217\u7684\u5168\u5bf9\u5168\u6bd4\u8f83\u3002\u5b83\u6700\u9002\u5408\u7528\u4e8e\u53ef\u80fd\u5177\u6709\u5927\u91cd\u6392\u7684\u9ad8\u5ea6\u76f8\u4f3c\u5e8f\u5217\u3002\u5e38\u89c1\u7684\u4f8b\u5b50\u662f\uff1a\u6bd4\u8f83\u4e24\u4e2a\u672a\u5b8c\u6210\u7684\u9e1f\u67aa\u5f0f\u6d4b\u5e8f\u7ec4\u4ef6\uff0c\u5c06\u672a\u5b8c\u6210\u7684\u6d4b\u5e8f\u7ec4\u4ef6\u6620\u5c04\u5230\u5b8c\u6210\u7684\u57fa\u56e0\u7ec4\uff0c\u4ee5\u53ca\u6bd4\u8f83\u4e24\u4e2a\u53ef\u80fd\u6709\u5927\u91cd\u6392\u548c\u91cd\u590d\u7684\u76f8\u5f53\u76f8\u4f3c\u7684\u57fa\u56e0\u7ec4\u3002<\/p>\n\n\n\n<p><strong>$ nucmer -p align ref.fasta contig.fasta<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong># nucmer -p [out_index] [ref] [query]<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong># -p|prefix\uff1aSet the prefix of the output files (default &#8220;out&#8221;)<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong># &#8211;mum: Use anchor matches that are unique in both the reference and query<\/strong><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005335547_11009946-F551-454d-8C60-17BF0F463487-1.png?resize=640%2C178\" alt=\"\" class=\"wp-image-61798\" width=\"640\" height=\"178\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005335547_11009946-F551-454d-8C60-17BF0F463487-1.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005335547_11009946-F551-454d-8C60-17BF0F463487-1.png?resize=300%2C83 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u56fe2 \u6bd4\u5bf9\u8fc7\u7a0b<\/p>\n\n\n\n<p>\u7ed3\u679c\u6587\u4ef6\u4f1a\u751f\u6210\u4e00\u4e2adelta\u4e3a\u540e\u7f00\u7684\u6587\u4ef6\uff0c\u8ba9\u6211\u4eec\u6253\u5f00\u5b83\u770b\u770b\uff1a<\/p>\n\n\n\n<p><strong>$ less align.delta<\/strong><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005348227_9C11547E-CF13-4491-A68E-0FC9A08390A5-1.png?resize=640%2C237\" alt=\"\" class=\"wp-image-61799\" width=\"640\" height=\"237\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005348227_9C11547E-CF13-4491-A68E-0FC9A08390A5-1.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005348227_9C11547E-CF13-4491-A68E-0FC9A08390A5-1.png?resize=300%2C111 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u56fe3 nucmer\u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n<ul>\n<li>\u6587\u4ef6\u7b2c\u4e00\u884c\u662f\u4e24\u4e2a\u9700\u8981\u6bd4\u8f83\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217fasta\u6587\u4ef6\u7684\u7edd\u5bf9\u8def\u5f84\u3002<\/li>\n\n\n\n<li>\u7b2c\u4e8c\u884c\u662f\u6bd4\u5bf9\u7c7b\u578b\uff0c\u53ef\u4ee5\u662fNUCMER\u6216PROMER\u3002<\/li>\n\n\n\n<li>\u7b2c\u4e09\u884c\u5f80\u540e\u662f\u6bd4\u5bf9\u7ed3\u679c\u3002\u6bcf\u4e2a\u6bd4\u5bf9\u7ed3\u679c\u4ee5\u884c\u9996\u4e3a &gt; \u53f7\u5f00\u5934\uff0c\u6574\u884c\u4e3a 0 \u7ed3\u5c3e\u3002<\/li>\n\n\n\n<li>\u6bd4\u5bf9\u7ed3\u679c\u7b2c\u4e00\u884c\u4ee5 &gt; \u53f7\u5f00\u5934\uff0c\u540e\u9762\u5305\u542b\u7a7a\u683c\u5206\u5272\u76844\u5217\uff0c\u5206\u522b\u662f\uff1areference\u5e8f\u5217 ID\u3001query\u5e8f\u5217ID\u3001\u8be5reference\u5e8f\u5217\u957f\u5ea6\u3001\u8be5query\u5e8f\u5217\u957f\u5ea6\u3002<\/li>\n\n\n\n<li>\u6bd4\u5bf9\u7ed3\u679c\u7b2c\u4e8c\u884c\u5305\u542b\u7a7a\u683c\u5206\u5272\u76847\u5217\u6570\u503c\uff0c\u5206\u522b\u662f\uff1areference\u5e8f\u5217\u6bd4\u5bf9\u8d77\u59cb\u4f4d\u70b9\u3001 reference\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u675f\u4f4d\u70b9\u3001query\u5e8f\u5217\u6bd4\u5bf9\u8d77\u59cb\u4f4d\u70b9\u3001query\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u675f\u4f4d\u70b9\u3001\u9519\u914d\u4f4d\u70b9\u6570\u3001\u4e0d\u76f8\u4f3c\u4f4d\u70b9\u6570\u3001\u975e\u5b57\u6bcd\u5b57\u7b26\u4e2a\u6570\u3002<\/li>\n\n\n\n<li>\u7b2c\u4e09\u884c\u5f80\u540e\u662fDelta\u503c\uff0c\u8868\u793a\u79bb\u4e0b\u4e00\u4e2aIDNEL\u4e4b\u95f4\u7684\u8ddd\u79bb\u3002<\/li>\n<\/ul>\n\n\n\n<p>2\u3001\u8fc7\u6ee4<\/p>\n\n\n\n<p>\u5e8f\u5217\u4e2d\u7684\u91cd\u590d\u5e8f\u5217\u53ef\u80fd\u4f1a\u63a9\u76d6\u53ef\u80fd\u7684SNP\uff0c\u6240\u4ee5\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528delta-filter\u53bb\u9664\u4e00\u5bf9\u591a\u3001\u591a\u5bf9\u591a\u4e2d\u7684\u5197\u4f59\u5339\u914d\u3002\u8fd9\u91cc\u7684\u7ed3\u679c\u4f1a\u6bd4\u8f83\u6666\u6da9\u96be\u61c2\uff0c\u6211\u4eec\u540e\u9762\u53ef\u4ee5\u8fdb\u884c\u53ef\u89c6\u5316\u3002<\/p>\n\n\n\n<p><strong>$ delta-filter -1 -i 90 -q -r align.delta &gt; align.filter.delta<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u5e38\u7528\u793a\u4f8b\uff1a<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>$ delta-filter -i 90 -l 2000 -m out.delta &gt; out.f.delta<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u5e38\u7528\u53c2\u6570\uff1a<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-i &lt;float&gt; &nbsp;&nbsp;&nbsp;default\uff1a0<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u8be5\u53c2\u6570\u7684\u503c\u5fc5\u987b\u8bbe\u5b9a\u4e3a0~100\uff0c\u8868\u793a\u8fc7\u6ee4\u6389Identity\u4f4e\u4e8e\u6b64\u503c\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-l &lt;float&gt; &nbsp;&nbsp;&nbsp;default: 0<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u8fc7\u6ee4\u6389\u5339\u914d\u533a\u57df\u957f\u5ea6\u4f4e\u4e8e\u6b64\u503c\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-u &lt;float&gt; &nbsp;&nbsp;&nbsp;default: 0<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u8981\u6c42\u6bd4\u5bf9\u533a\u57df\u7684unique\u5e8f\u5217\u6240\u5360\u7684\u767e\u5206\u6bd4\u4e0d\u4f4e\u4e8e\u6b64\u503c\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-q<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u5bf9query\u5e8f\u5217\u7684\u6bcf\u4e2a\u6bd4\u5bf9\u4f4d\u70b9\uff0c\u4ec5\u9009\u62e9\u5176\u5728reference\u5e8f\u5217\u4e0a\u7684\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u82e5\u9700\u8981\u5c06contigs\u5e8f\u5217\u6216reads\u5b9a\u4f4d\u5230reference genome\u4e0a\uff0c\u8003\u8651\u4f7f\u7528-q\u53c2\u6570\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-r<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u5bf9reference\u5e8f\u5217\u7684\u6bcf\u4e2a\u6bd4\u5bf9\u4f4d\u70b9\uff0c\u4ec5\u9009\u62e9\u5176\u5728query\u5e8f\u5217\u7684\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-g<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u52a0\u5165\u8be5\u53c2\u6570\uff0c\u5219\u8981\u6c42\u6bd4\u5bf9\u533a\u57df\u5185\u90e8\u7684maximal matches\u4e4b\u95f4\u4e0d\u80fd\u6709\u91cd\u6392\uff0c\u5982<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u79fb\u4f4d\u3001\u5012\u4f4d\u7b49\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-m<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u52a0\u5165\u8be5\u53c2\u6570\uff0c\u8868\u793a\u53d6-q\u548c-r\u53c2\u6570\u7684\u5e76\u96c6\u3002\u4e00\u4e2aquery\u4f4d\u70b9\u53ef\u80fd\u6bd4\u5bf9\u5230ref\u4e0a\u591a<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4e2a\u4f4d\u70b9\uff0c\u4ec5\u4fdd\u7559\u5176\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\uff1b\u4e00\u4e2aref\u4f4d\u70b9\u4e5f\u53ef\u80fd\u6bd4\u5bf9\u5230query\u4e0a\u591a\u4e2a\u4f4d\u70b9\uff0c\u4ec5<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4fdd\u7559\u5176\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\uff1b\u4ee5\u4e0a\u4e24\u4e2a\u5904\u7406\u65b9\u6cd5\u7684\u8f93\u5165\u4fe1\u606f\u662f\u4e00\u6837\u7684\uff0c\u90fd\u662f\u6240\u6709\u7684\u6bd4\u5bf9\u7ed3\u679c\uff1b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u82e5\u4f7f\u7528 -q -r \u53c2\u6570\uff0c\u5219\u662f\u5148\u8fd0\u7528\u7b2c\u4e00\u79cd\u65b9\u6cd5\u5904\u7406\uff0c\u5f97\u5230\u7684\u7ed3\u679c\u518d\u8fd0\u7528\u7b2c\u4e8c\u79cd\u65b9\u6cd5<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u5904\u7406\uff0c\u5176\u7ed3\u679c\u76f8\u6bd4\u4e8e\u4ec5\u4f7f\u7528 -m \u53c2\u6570\uff0c\u8f93\u51fa\u7684\u6bd4\u5bf9\u7ed3\u679c\u66f4\u5c11\u3002\u4e00\u822c\u60c5\u51b5\u4e0b\uff0c\u4f7f\u7528 -m<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u53c2\u6570\u662f\u6700\u4f18\u7684\u65b9\u6cd5\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-1<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>&nbsp;&nbsp;&nbsp;&nbsp;\u52a0\u5165\u8be5\u53c2\u6570\uff0c\u8868\u793a\u53d6-q\u548c-r\u53c2\u6570\u7684\u4ea4\u96c6\u3002\u4e00\u4e2aquery\u4f4d\u70b9\u53ef\u80fd\u6bd4\u5bf9\u5230ref\u4e0a\u591a<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4e2a\u4f4d\u70b9\uff0c\u4e00\u4e2aref\u4f4d\u70b9\u4e5f\u53ef\u80fd\u6bd4\u5bf9\u5230query\u4e0a\u591a\u4e2a\u4f4d\u70b9\uff1b\u52a0\u5165\u8be5\u53c2\u6570\uff0c\u8868\u793a\u8981\u6c42query<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4f4d\u70b9\u548cref\u4f4d\u70b9\u80fd\u76f8\u4e92\u6bd4\u5bf9\u4e0a\uff0c\u4e14\u5b83\u4eec\u662f\u76f8\u4e92\u6700\u4f73\u6bd4\u5bf9\uff1b\u82e5\u4f7f\u7528 -q -r \u53c2\u6570\uff0c\u5f97\u5230\u7684<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u867d\u7136\u4e5f\u662f1\u5bf91\u7684\u6bd4\u5bf9\u7ed3\u679c\uff0c\u4f46\u5176\u4e0d\u4e00\u5b9a\u662f\u76f8\u4e92\u6700\u4f73\u6bd4\u5bf9\uff0c-1\u53c2\u6570\u7684\u8f93\u51fa\u5bf9\u7ed3\u679c\u66f4\u5c11\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u82e5\u9700\u8981\u5f97\u5230SNP\u7ed3\u679c\uff0c\u5219\u9700\u8981\u52a0\u5165\u8be5\u53c2\u6570\u6765\u786e\u4fdd\u7ed3\u679c\u7684\u51c6\u786e\u6027\u3002<\/strong><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005364779_F1AC3B2A-42CD-4128-A9E6-BCA98FBB50D9-1.png?resize=640%2C227\" alt=\"\" class=\"wp-image-61800\" width=\"640\" height=\"227\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005364779_F1AC3B2A-42CD-4128-A9E6-BCA98FBB50D9-1.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005364779_F1AC3B2A-42CD-4128-A9E6-BCA98FBB50D9-1.png?resize=300%2C107 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u56fe4 \u8fc7\u6ee4\u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n<p>3\u3001\u5750\u6807\u8f6c\u6362<\/p>\n\n\n\n<p>\u4f7f\u7528show-coords\u811a\u672c\u53ef\u4ee5\u5c06delta\u6587\u4ef6\u8f6c\u6362\u4e3a\u6613\u8bfb\u7684\u5339\u914d\u5750\u6807\uff0c\u8fd9\u4e00\u90e8\u5206\u53ef\u4ee5\u8fdb\u884c\u4e24\u4e2a\u57fa\u56e0\u7ec4\u7684\u5171\u7ebf\u6027\u5206\u6790\u3002<\/p>\n\n\n\n<p><strong>$ show-coords -c -r align.filter.delta &gt; align.filter.coords<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>#-c \u8f93\u51fa\u7ed3\u679c\u4e2d\u591a\u5904\u8986\u76d6\u6bd4\u8fd9\u4e00\u5217<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>#-r \u5bf9\u7ed3\u679c\u8fdb\u884c\u6392\u5e8f\u8f93\u51fa<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u7ed3\u679c\u6587\u4ef6\u4e3aalign.filter.coords\uff0c\u8ba9\u6211\u4eec\u6765\u770b\u4e00\u770b\u7ed3\u679c\u5982\u4f55\uff1a<\/p>\n\n\n\n<p><strong>$ less align.filter.coords<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>[S1]\u548c[E1]\uff0c\u7b2c\u4e00\u4e2a\u57fa\u56e0\u7ec4\u4e2d\uff0c\u548c\u7b2c\u4e8c\u4e2a\u57fa\u56e0\u7ec4\u5bf9\u9f50\u7684\u533a\u57df\uff0cS1\u548cE1\u5206\u522b\u4e3a\u8fd9\u6bb5\u533a\u57df\u5728\u7b2c\u4e00\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u7684\u8d77\u59cb\u548c\u7ed3\u675f\u4f4d\u70b9\uff1b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>[S2]\u548c[E2]\uff0c\u7b2c\u4e8c\u4e2a\u57fa\u56e0\u7ec4\u4e2d\uff0c\u548c\u7b2c\u4e00\u4e2a\u57fa\u56e0\u7ec4\u5bf9\u9f50\u7684\u533a\u57df\uff0cS2\u548cE2\u5206\u522b\u4e3a\u8fd9\u6bb5\u533a\u57df\u5728\u7b2c\u4e8c\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u7684\u8d77\u59cb\u548c\u7ed3\u675f\u4f4d\u70b9\uff08\u5982\u679c\u8d77\u59cb\u4f4d\u70b9\u6bd4\u7ed3\u675f\u4f4d\u70b9\u7684\u6570\u503c\u5927\uff0c\u5219\u610f\u5473\u7740\u5728\u8fd9\u6bb5\u533a\u57df\u4e2d\u548c\u5176\u4e92\u8865\u94fe\u5bf9\u9f50\uff09\uff1b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>[LEN1]\u548c[LEN 2]\uff0c\u5206\u522b\u4e24\u4e2a\u57fa\u56e0\u7ec4\u4e2d\uff0c\u5bf9\u9f50\u533a\u57df\u7684\u957f\u5ea6\uff1b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>[% IDY]\uff0c\u4e24\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u5bf9\u9f50\u533a\u57df\u7684\u78b1\u57fa\u4e00\u81f4\u6027\uff0c\u5b8c\u5168\u4e00\u81f4\u5219\u662f100%\uff1b<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>[COV R]\u548c[COV Q]\uff0c\u8986\u76d6\u5ea6\u3002<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>[TAGS]\uff0c\u57fa\u56e0\u7ec4\u4e2d\u4e24\u6bb5\u5b58\u5728\u5171\u7ebf\u6027\u533a\u57df\u7684\u5e8f\u5217\u7684\u540d\u79f0\uff1b<\/strong><strong><\/strong><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005377910_842E3154-F424-40f2-B9F5-C6FFD27216FE-1.png?resize=640%2C352\" alt=\"\" class=\"wp-image-61801\" width=\"640\" height=\"352\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005377910_842E3154-F424-40f2-B9F5-C6FFD27216FE-1.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005377910_842E3154-F424-40f2-B9F5-C6FFD27216FE-1.png?resize=300%2C165 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u56fe5 \u5750\u6807\u8f6c\u6362\u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n<p>4\u3001Call Snp<\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528show-snps\u663e\u793a\u8fc7\u6ee4\u540e\u7684delta\u6587\u4ef6\u4e2d\u5339\u914d\u7684SNP\uff1a<\/p>\n\n\n\n<p><strong>$ show-snps -C &nbsp;-I -T -r -l align.filter.delta &gt; align.filter.snp<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>USAGE: show-snps &nbsp;[options] &nbsp;&lt;deltafile&gt;<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-C<\/strong><strong> <\/strong><strong>\u4e0d\u8981\u62a5\u544a\u5177\u6709\u6a21\u7cca\u6620\u5c04\u7684\u6bd4\u5bf9\u4e2d\u7684SNP\uff0c\u5373\u53ea\u62a5\u544a[R]\u548c[Q]\u5217\u7b49\u4e8e0\u7684SNP\uff0c\u800c\u4e0d\u8f93\u51fa\u8fd9\u4e9b\u5217<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-h<\/strong><strong> <\/strong><strong>\u663e\u793a\u5e2e\u52a9\u4fe1\u606f<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-H<\/strong><strong> <\/strong><strong>\u4e0d\u6253\u5370\u8f93\u51fa\u6807\u9898<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-I<\/strong><strong> <\/strong><strong>\u4e0d\u62a5\u544aindels<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-l<\/strong><strong> <\/strong><strong>\u5728\u8f93\u51fa\u4e2d\u5305\u542b\u5e8f\u5217\u957f\u5ea6\u4fe1\u606f<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-q<\/strong><strong> <\/strong><strong>\u6309\u67e5\u8be2ID\u548cSNP\u4f4d\u7f6e\u5bf9\u8f93\u51fa\u884c\u8fdb\u884c\u6392\u5e8f<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-r<\/strong><strong> <\/strong><strong>\u6309\u53c2\u8003ID\u548cSNP\u4f4d\u7f6e\u5bf9\u8f93\u51fa\u884c\u8fdb\u884c\u6392\u5e8f<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-S<\/strong><strong> <\/strong><strong>\u901a\u8fc7\u5411stdin\u4f20\u9012\u201c\u663e\u793a\u5750\u6807\u201d\u884c\u6765\u6307\u5b9a\u8981\u62a5\u544a\u7684\u5bf9\u9f50\u65b9\u5f0f<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-T<\/strong><strong> <\/strong><strong>\u5207\u6362\u5230\u5236\u8868\u7b26\u5206\u9694\u683c\u5f0f<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>-x <\/strong><strong><\/strong><strong>int\u5728\u8f93\u51fa\u4e2d\u5305\u542b\u5468\u56f4SNP\u4e0a\u4e0b\u6587\u7684x\u4e2a\u5b57\u7b26\uff0c\u9ed8\u8ba4\u4e3a0<\/strong><strong><\/strong><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005387908_F1C3FC3A-5E97-467d-9691-6C2F51C55FF4.png?resize=640%2C202\" alt=\"\" class=\"wp-image-61802\" width=\"640\" height=\"202\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005387908_F1C3FC3A-5E97-467d-9691-6C2F51C55FF4.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/11\/1732005387908_F1C3FC3A-5E97-467d-9691-6C2F51C55FF4.png?resize=300%2C95 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u56fe6 Show-snps\u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n<p>\u4ee5\u4e0a\u7ed3\u679c\u6587\u4ef6\u5c31\u662fSNP\u7ed3\u679c\u6587\u4ef6\u5566\uff0c\u6211\u4eec\u53ef\u4ee5\u5c06\u5176\u8f6c\u5316\u4e3aVCF\u6587\u4ef6\uff0c\u518d\u8f6c\u6362\u4e3a\u77e9\u9635\uff0c\u63d0\u53d6\u51fafasta\u4e4b\u540e\u8fd8\u53ef\u4ee5\u8fdb\u884c\u5168\u57fa\u56e0\u7ec4SNP\u7684\u7cfb\u7edf\u53d1\u80b2\u5206\u6790~\u5c0f\u5e08\u59b9\u5728\u5f80\u671f\u7684\u516c\u4f17\u53f7\u4e5f\u6709\u63d0\u5230\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u7684\u4e00\u7ad9\u5f0f\u6d41\u7a0b\uff0c\u6b22\u8fce\u67e5\u9605\u3002<\/p>\n\n\n\n<h1 class=\"wp-block-heading\"><strong>\u4e09\u3001\u5c0f\u7ed3<\/strong><strong><\/strong><\/h1>\n\n\n\n<p>Mummer\u5de5\u5177\u4e3b\u8981\u6709\u4e24\u5927\u5e94\u7528\u573a\u666f\uff0c\u4e00\u662f\u8fdb\u884c\u57fa\u56e0\u7ec4\u4e4b\u95f4\u7684\u5171\u7ebf\u6027\u68c0\u6d4b\uff0c\u4e8c\u5c31\u662f\u5168\u57fa\u56e0\u7ec4\u8303\u56f4\u7684SNP\u68c0\u6d4b\uff0c\u4e0e\u5e38\u89c4gatk\u6216bcftools\u7684call snp\u6d41\u7a0b\u4e0d\u540c\uff0cMummer\u5de5\u5177\u91c7\u7528\u7684\u662f\u540e\u7f00\u6811\u7b97\u6cd5\uff0c\u901f\u5ea6\u65b9\u9762\u4f1a\u5feb\u5f88\u591a\u3002<\/p>\n\n\n\n<p>\u7cfb\u7edf\u53d1\u80b2\u76f8\u5173\u7684\u57fa\u56e0\u7ec4\u4e4b\u95f4\u65e2\u5b58\u5728\u4fdd\u5b88\u6027\u53c8\u5b58\u5728\u53ef\u53d8\u6027\u3002\u6709\u4e9b\u5e8f\u5217\u7247\u6bb5\u7684\u6570\u76ee\u4ee5\u53ca\u987a\u5e8f\u5177\u6709\u4fdd\u5b88\u6027\uff0c\u8fd9\u79cd\u4fdd\u5b88\u6027\u53ef\u4ee5\u4f7f\u7528\u5171\u7ebf\u6027\u6765\u8fdb\u884c\u63cf\u8ff0\u3002\u5171\u7ebf\u6027\u4e3b\u8981\u5f3a\u8c03\u4e24\u65b9\u9762\uff0c\u4e00\u662f\u5e8f\u5217\u7684\u540c\u6e90\u6027\uff0c\u4e8c\u662f\u5e8f\u5217\u7247\u6bb5\u7684\u6392\u5217\u987a\u5e8f\u3002\u540c\u65f6\u5373\u4f7f\u5f88\u8fd1\u7f18\u7684\u57fa\u56e0\u7ec4\u4e5f\u53ef\u80fd\u5b58\u5728\u5927\u91cf\u7684\u53d8\u5f02\u548c\u591a\u6001\u6027\uff0c\u8fd9\u79cd\u53d8\u5f02\u53ef\u80fd\u6784\u6210\u4e86\u4e0d\u540c\u4e2a\u4f53\u4e0e\u7fa4\u4f53\u6027\u72b6\u5dee\u5f02\u7684\u57fa\u7840\u3002\u5355\u6838\u82f7\u9178\u591a\u6001\u6027(single-nucleotide polymorphism\uff0cSNP)\u662f\u6307\u7531\u4e8e\u5355\u4e2a\u6838\u82f7\u9178\u4f4d\u7f6e\u4e0a\u5b58\u5728\u8f6c\u6362\u6216\u98a0\u6362\u7b49\u53d8\u5f02\u6240\u5f15\u8d77\u7684DNA\u5e8f\u5217\u591a\u6001\u6027\uff0c\u5e38\u7528\u6765\u7814\u7a76\u8fd1\u7f18\u7269\u79cd\u57fa\u56e0\u7ec4\u7684\u8fdb\u5316\u3002<\/p>\n\n\n\n<p>\u4eca\u5929\u5c0f\u5e08\u59b9\u7ed9\u5927\u5bb6\u91cd\u70b9\u4ecb\u7ecd\u7684\u662fSNP\u68c0\u6d4b\uff0c\u5f53\u7136\u5927\u5bb6\u4e5f\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u7684\u9700\u6c42\u548c\u7814\u7a76\u76ee\u6807\u4fee\u6539\u548c\u6269\u5c55\u8fd9\u4e9b\u4ee3\u7801\u54e6\uff01\uff01\u600e\u4e48\u6837\uff0c\u4f60\u5b66\u4f1a\u4e86\u561b\uff01\uff1f<\/p>\n\n\n\n<p><strong>\u540c\u5b66\u4eec\u5982\u679c\u89c9\u5f97\u81ea\u5df1\u5199\u4ee3\u7801\u9ebb\u70e6\uff0c\u53ef\u4ee5\u4f53\u9a8c\u4e00\u4e0b\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\uff0c\u53ea\u9700\u8f93\u5165\u6570\u636e\uff0c\u5373\u53ef\u8f7b\u677e\u751f\u6210\u6240\u9700\u56fe\u8868\u3002\u7acb\u5373\u8bbf\u95ee\u4e91\u751f\u4fe1\uff08http:\/\/www.biocloudservice.com\/home.html\uff09\uff0c\u5f00\u542f\u4fbf\u6377\u7684\u751f\u4fe1\u4e4b\u65c5\uff01<\/strong><strong><\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u55e8\uff0c\u6211\u662f\u5c0f\u5e08\u59b9\uff0c\u5f88\u9ad8\u5174\u80fd\u591f\u548c\u5927\u5bb6\u4e00\u8d77\u6765\u5b66\u4e60\u751f\u7269\u4fe1\u606f\u5b66\u3002\u5982\u679c\u8bf4\u8001\u5e08\u8ba9\u4f60\u53bb\u627e\u4e24\u4e2a\u4e2a\u4f53\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u60c5\u51b5\uff0c\u76f8\u4fe1\u5f88\u591a\u4eba\u90fd [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61790"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=61790"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61790\/revisions"}],"predecessor-version":[{"id":61803,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61790\/revisions\/61803"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61790"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61790"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61790"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}