{"id":61804,"date":"2024-11-21T15:11:21","date_gmt":"2024-11-21T07:11:21","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61804"},"modified":"2024-11-21T15:11:21","modified_gmt":"2024-11-21T07:11:21","slug":"snippy%ef%bc%9a%e4%b8%80%e6%9d%a1%e5%91%bd%e4%bb%a4%e4%bb%8erawdata%e5%88%b0%e8%bf%9b%e5%8c%96%e6%a0%91%ef%bc%8c%e4%b8%80%e7%ab%99%e5%bc%8f%e8%a7%a3%e5%86%b3%e4%bd%a0%e7%9a%84%e5%85%a8%e5%9f%ba","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61804","title":{"rendered":"Snippy\uff1a\u4e00\u6761\u547d\u4ee4\u4ecerawdata\u5230\u8fdb\u5316\u6811\uff0c\u4e00\u7ad9\u5f0f\u89e3\u51b3\u4f60\u7684\u5168\u57fa\u56e0\u7ec4SNP\u5206\u6790\uff01"},"content":{"rendered":"\n

<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\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\u524d\u9762\u51e0\u5929\u5728\u5916\u7f51\u4e0a\u770b\u5230\u4e00\u4e2a\u9488\u5bf9\u7ec6\u83cc\u57fa\u56e0\u7ec4SNP\u9274\u5b9a\u5de5\u5177\u7684\u8c03\u67e5\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe1 SNP\u68c0\u6d4b\u5de5\u5177\u6d41<\/p>\n\n\n\n

\u4ece\u56fe\u4e2d\u53ef\u4ee5\u770b\u51fasnippy\u8fd8\u662f\u6bd4\u8f83\u53d7\u6b22\u8fce\u7684\uff0c\u63a5\u53e3\u4e5f\u5f88\u7b80\u5355\u3002\u8fd9\u6b21\u89e3\u8bfb\u7684\u4e3b\u89d2\u662fsnippy\uff0c\u4f7f\u7528\u8d77\u6765\u786e\u5b9e\u5f88\u65b9\u4fbf\uff0c\u4e00\u6761\u547d\u4ee4\u53ef\u4ee5\u89e3\u51b3\u6211\u4eec\u4ecesra\u5230vcf\u5230\u7684\u95ee\u9898\uff0c\u5f53\u7136\u5176\u4e2d\u4f7f\u7528\u7684\u5de5\u5177\u5f88\u591a\u4e86\uff0c\u4f46\u662f\u90fd\u88ab\u5c01\u88c5\u5728\u811a\u672c\u91cc\u4e86\u3002\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

    \n
  1. \u6d4b\u5e8f\u6570\u636e\u4e0e\u53c2\u8003\u57fa\u56e0\u7ec4\u6bd4\u5bf9\u83b7\u5f97sam\u3001bam\u6570\u636e<\/li>\n\n\n\n
  2. Samtools\u3001GATK\u3001freebayes\u7b49\u8f6f\u4ef6\u5229\u7528bam\u6587\u4ef6\u83b7\u5f97VCF<\/li>\n\n\n\n
  3. Snpeff\u5bf9VCF\u6587\u4ef6\u8fdb\u884c\u6ce8\u91ca<\/li>\n\n\n\n
  4. Vcf\u6587\u4ef6\u8f6c\u6362\u6210fasta\u683c\u5f0f\u4f7f\u7528IQtree\u3001mega\u7b49\u8f6f\u4ef6\u6784\u5efa\u7cfb\u7edf\u53d1\u80b2\u6811<\/li>\n<\/ol>\n\n\n\n

    Snippy \u662f\u4e00\u4e2a\u7528\u4e8e\u5feb\u901f\u53d1\u73b0\u5355\u500d\u4f53\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0e\u4e0b\u4e00\u4ee3\u6d4b\u5e8f\uff08NGS\uff09\u5e8f\u5217\u8bfb\u53d6\u4e4b\u95f4\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff08SNPs\uff09\u548c\u63d2\u5165\/\u5220\u9664\uff08indels\uff09\u7684\u5de5\u5177\u3002\u5b83\u8bbe\u8ba1\u7528\u4e8e\u5728\u5355\u4e2a\u8ba1\u7b97\u673a\u4e0a\u5229\u7528\u5c3d\u53ef\u80fd\u591a\u7684CPU\u6838\u5fc3\uff0c\u4ee5\u5b9e\u73b0\u9ad8\u901f\u5904\u7406\u3002Snippy \u7531 Torsten Seemann \u5f00\u53d1\uff0c\u662f\u4e00\u4e2a\u5e7f\u6cdb\u5e94\u7528\u4e8e\u57fa\u56e0\u7ec4\u53d8\u5f02\u5206\u6790\u7684\u5f00\u6e90\u5de5\u5177\u3002\u4e0b\u9762\u5c0f\u5e08\u59b9\u5c31\u5e96\u4e01\u89e3\u725b\u822c\u89e3\u8bfb\u4e0b\u8fd9\u4e9b\u6d41\u7a0b\u5de5\u5177\u662f\u5982\u4f55\u5de5\u4f5c\u7684\uff0c\u6d41\u7a0b\u53c8\u662f\u5982\u4f55\u8bbe\u8ba1\u7684\uff0c\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\u3002\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>\n\n\n\n

    \u4e00\u3001\u4e0b\u8f7d\u548c\u5b89\u88c5<\/strong><\/strong><\/p>\n\n\n\n

    1\u3001\u5b89\u88c5\u90e8\u5206<\/p>\n\n\n\n

    Conda\u5b89\u88c5<\/strong><\/strong><\/p>\n\n\n\n

    snippy=4.6.0\u4e3a\u4f5c\u8005\u63a8\u8350\u7684\u7248\u672c\uff0c\u800csnippy=4.6.0\u517c\u5bb9snpeff=5.0\uff0c\u66f4\u9ad8\u7684\u7248\u672c\u5219\u53ef\u80fd\u62a5\u9519\u3002\u5b89\u88c5\u540e\uff0c\u5982\u679c\u8fd0\u884csnippy\u65f6\u51fa\u73b0\u4e00\u4e9b\u6267\u884c\u4e0a\u7684\u95ee\u9898\uff0c\u9700\u68c0\u67e5\u6240\u4f9d\u8d56\u7684\u8f6f\u4ef6\u7248\u672c\u3002<\/p>\n\n\n\n

    $ conda install -c conda-forge -c bioconda -c defaults snippy<\/strong><\/strong><\/p>\n\n\n\n

    Mac\u5b89\u88c5<\/strong><\/strong><\/p>\n\n\n\n

    $ brew install brewsci\/bio\/snippy<\/strong><\/strong><\/p>\n\n\n\n

    Github\u5b89\u88c5\u6700\u65b0\u7248<\/strong><\/strong><\/p>\n\n\n\n

    $ cd $HOME<\/strong><\/strong><\/p>\n\n\n\n

    $ git clone https:\/\/github.com\/tseemann\/snippy.git<\/strong><\/strong><\/p>\n\n\n\n

    $ HOME\/snippy\/bin\/snippy –help<\/strong><\/strong><\/p>\n\n\n\n

    # \u6dfb\u52a0snippy\u4ee5\u53ca\u4f9d\u8d56\u5e93\u7684\u8def\u5f84\u5230\u73af\u5883\u53d8\u91cf\u4e2d\uff0c\u53ef\u76f4\u63a5\u8c03\u7528snippy<\/strong><\/strong><\/p>\n\n\n\n

    $ echo ‘export PATH=”$HOME\/repos\/snippy\/bin:$HOME\/repos\/snippy\/binary\/linux:$PATH”‘ >> ~\/.bashrc<\/strong><\/strong><\/p>\n\n\n\n

    $ source ~\/.bashrc<\/strong><\/strong><\/p>\n\n\n\n

    2\u3001\u6838\u9a8c\u5b89\u88c5\u662f\u5426\u5b8c\u6210<\/p>\n\n\n\n

    \u68c0\u67e5\u5b89\u88c5\u8f6f\u4ef6\u7684\u7248\u672c<\/strong><\/strong><\/p>\n\n\n\n

    $ snippy –version<\/strong><\/strong><\/p>\n\n\n\n

    \u68c0\u67e5\u6240\u6709\u4f9d\u8d56\u9879\u662f\u5426\u5df2\u5b89\u88c5\u5e76\u6b63\u5e38\u5de5\u4f5c<\/strong><\/strong><\/p>\n\n\n\n

    $ snippy –check<\/strong><\/strong><\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe2 \u68c0\u67e5\u4f9d\u8d56\u9879<\/p>\n\n\n\n

    \u4e8c\u3001\u5e38\u7528\u547d\u4ee4<\/strong><\/strong><\/p>\n\n\n\n

    1\u3001Snippy-multi<\/p>\n\n\n\n

    Snippy\u5171\u6709\u4e09\u79cd\u8f93\u5165\u65b9\u5f0f\uff0c\u5206\u522b\u662ffastq\u3001\u62fc\u63a5\u597d\u7684fasta\u4ee5\u53ca\u6bd4\u5bf9\u597d\u7684bam\u6587\u4ef6<\/strong><\/strong><\/p>\n\n\n\n

    USAGE<\/strong><\/strong><\/p>\n\n\n\n

      snippy [options] –outdir <dir> –ref <ref> –R1 <R1.fq.gz> –R2 <R2.fq.gz><\/strong><\/strong><\/p>\n\n\n\n

      snippy [options] –outdir <dir> –ref <ref> –ctgs <contigs.fa><\/strong><\/strong><\/p>\n\n\n\n

      snippy [options] –outdir <dir> –ref <ref> –bam <reads.bam><\/strong><\/strong><\/p>\n\n\n\n

    \u4ee5\u4e0a\u662f\u5355\u4e2a\u6587\u4ef6\u7684\u8f93\u5165\u65b9\u5f0f\uff0c\u5982\u679c\u4f60\u6709\u591a\u4e2a\u6587\u4ef6\uff0c\u53ef\u4ee5\u7528snippy-multi\u547d\u4ee4\uff1a<\/strong><\/strong><\/p>\n\n\n\n

    # input.tab = ID R1 [R2]<\/strong><\/strong><\/p>\n\n\n\n

    Isolate1<\/strong> <\/strong>\/path\/to\/R1.fq.gz<\/strong> <\/strong>\/path\/to\/R2.fq.gz<\/strong><\/strong><\/p>\n\n\n\n

    Isolate1b<\/strong> <\/strong>\/path\/to\/R1.fastq.gz<\/strong> <\/strong>\/path\/to\/R2.fastq.gz<\/strong><\/strong><\/p>\n\n\n\n

    Isolate1c<\/strong> <\/strong>\/path\/to\/R1.fa<\/strong> <\/strong><\/strong>\/path\/to\/R2.fa<\/strong><\/strong><\/p>\n\n\n\n

    # \u5355\u7aef\u8bfb\u53d6\u4e5f\u652f\u6301<\/strong><\/strong><\/p>\n\n\n\n

    Isolate2<\/strong> <\/strong>\/path\/to\/SE.fq.gz<\/strong><\/strong><\/p>\n\n\n\n

    Isolate2b<\/strong> <\/strong>\/path\/to\/iontorrent.fastq<\/strong><\/strong><\/p>\n\n\n\n

    # \u6216\u5df2\u7ecf\u7ec4\u88c5\u7684\u5143\u4ef6\uff0c\u5982\u679c\u4f60\u6ca1\u6709\u8bfb\u53d6\u6570\u636e<\/strong><\/strong><\/p>\n\n\n\n

    Isolate3<\/strong> <\/strong>\/path\/to\/contigs.fa<\/strong><\/strong><\/p>\n\n\n\n

    Isolate3b<\/strong> <\/strong>\/path\/to\/reference.fna.gz<\/strong><\/strong><\/p>\n\n\n\n

    \u4e3a\u4e86\u4fbf\u4e8e\u5c06\u591a\u4e2a\u6d4b\u5e8f\u6570\u636e\u6bd4\u5bf9\u5230\u53c2\u8003\u57fa\u56e0\u7ec4\uff0c\u63a8\u8350\u4f7f\u7528 snippy-multi\u3002\u8fd9\u4e2a\u811a\u672c\u7684\u8f93\u5165\u6587\u4ef6\u9700\u8981\u7531\u5236\u8868\u7b26\uff08tab\uff09\u5206\u5272\uff0c\u8f93\u5165\u6587\u4ef6\u53ef\u4ee5\u662f\u5355\u7aef\u3001\u53cc\u7aef\u548c\u7ec4\u88c5\u7684\u6d4b\u5e8f\u6570\u636e\uff08paired-end reads, single-end reads, \u548c assembled contigs\uff09\u3002\u6309\u7167github\u7684\u8bf4\u660e\uff0c\u83cc\u682a\u548cfasta\u4e4b\u95f4\u6709\u4e2aTab\u952e\u5c31\u53ef\u4ee5\u4e86\u3002\u4ee5\u4e0b\u62ff\u7ec4\u88c5\u540e\u7684contig\u4f5c\u4e3a\u4f8b\u5b50\uff0c\u8fd9\u91cc\u7684\u8f93\u5165\u662f\u4e03\u4e2a\u7ec4\u88c5\u597d\u7684contig\u6587\u4ef6\uff1a<\/p>\n\n\n\n

    $ less input.tab<\/strong><\/strong><\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe3 input.tab\u6587\u4ef6\u5185\u5bb9<\/p>\n\n\n\n

    \u7136\u540e\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\u6765\u751f\u6210\u8f93\u51fa\u811a\u672c\u3002\u7b2c\u4e00\u4e2a\u53c2\u6570\u5e94\u4e3a input.tab \u6587\u4ef6\u3002\u5176\u4f59\u53c2\u6570\u5e94\u8be5\u662f\u5171\u4eab\u7684 snippy \u53c2\u6570\u3002<\/p>\n\n\n\n

    $ snippy-multi input.tab –ref ref.fna –cpus 16 > runme.sh<\/strong><\/strong><\/p>\n\n\n\n

    \u68c0\u67e5\u811a\u672c\u662f\u5426\u5408\u7406\uff0c\u6700\u540e\u4e00\u884c\u5b83\u8fd8\u4f1a\u5728\u6700\u540e\u8fd0\u884c snippy-core \u4ee5\u751f\u6210\u6838\u5fc3\u57fa\u56e0\u7ec4 SNP \u5bf9\u9f50\u6587\u4ef6 core.*\uff1a<\/p>\n\n\n\n

    $ less runme.sh<\/strong><\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe4 \u8fd0\u884c\u811a\u672c<\/p>\n\n\n\n

    \u8fd0\u884c\u811a\u672c\uff1a<\/strong><\/p>\n\n\n\n

    $ sh .\/runme.sh<\/strong><\/strong><\/p>\n\n\n\n

    \u7ed3\u679c\u6587\u4ef6\u6210\u529f\u751f\u6210\u4e86\uff0c\u8ba9\u6211\u4eec\u6253\u5f00\u4e00\u4e2a\u6765\u770b\u770b\uff1a<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe5 \u8f93\u51fa\u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n

    \u76f8\u5173\u7684\u7ed3\u679c\u6587\u4ef6\u63cf\u8ff0\u5982\u4e0b\uff1a<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe6 \u76f8\u5173\u6587\u4ef6\u63cf\u8ff0<\/p>\n\n\n\n

    2\u3001Snippy-core\uff1acore SNP\u7cfb\u7edf\u53d1\u80b2\u5206\u6790<\/p>\n\n\n\n

    \u5982\u679c\u8981\u5c06\u591a\u4e2a\u83cc\u682a\u6bd4\u5bf9\u5230\u540c\u4e00\u4e2a\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0a\uff0c\u53ef\u4ee5\u4ea7\u751f\u4e00\u4e2a\u201ccore SNP\u201d\u7684\u6bd4\u5bf9\uff0c\u53ef\u7528\u6765\u5efa\u7acb\u5177\u6709\u9ad8\u5ea6\u5206\u8fa8\u7387\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\uff08\u5ffd\u89c6\u53ef\u80fd\u7684\u57fa\u56e0\u91cd\u7ec4\uff09\u3002\u4e00\u4e2a\u6838\u5fc3\u4f4d\u70b9\u662f\u6307\u5b58\u5728\u4e8e\u6240\u6709\u7ec6\u83cc\u6837\u672c\u4e2d\u7684\u57fa\u56e0\u7ec4\u4f4d\u7f6e\u3002\u4e00\u4e2a\u6838\u5fc3\u4f4d\u70b9\u53ef\u4ee5\u5728\u6bcf\u4e2a\u7ec6\u83cc\u6837\u672c\u4e2d\u5177\u6709\u76f8\u540c\u7684\u6838\u82f7\u9178\uff0c\u4e5f\u53ef\u4ee5\u4e0d\u540c\u3002\u5982\u679c\u6211\u4eec\u5ffd\u7565\u7ec6\u83cc\u4e2d\u7684\u7684\u63d2\u5165\u548c\u7f3a\u5931\u7a81\u53d8\u7684\u590d\u6742\u6027\uff0c\u4ec5\u4f7f\u7528\u53d8\u5f02\u4f4d\u70b9\uff0c\u8fd9\u4e9b\u5c31\u662fcore SNP genome\u3002\u5176\u4e2dSnippy-core\u7684\u547d\u4ee4\u5df2\u7ecf\u5305\u542b\u5728\u4e86Snippy-multi\u7684\u811a\u672c\u4e2d\uff0c<\/p>\n\n\n\n

    $ snippy-core –ref ref.fa case1 case2 case3 case4 case5 case6 case7<\/strong><\/strong><\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe7 \u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n

    core.aln\uff1a<\/strong>\u8fd9\u662f\u4e00\u4e2a\u6838\u5fc3\u57fa\u56e0\u7ec4\u7684\u6bd4\u5bf9\u6587\u4ef6\uff0c\u5305\u542b\u6240\u6709\u6837\u672c\u7684\u6838\u5fc3\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002\u7528\u4e8e\u540e\u7eed\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\u6784\u5efa\u548c\u8fdb\u5316\u5173\u7cfb\u5206\u6790\u3002<\/p>\n\n\n\n

    core.full.aln<\/strong>\uff1a\u5305\u542b\u6240\u6709\u6837\u672c\u7684\u6240\u6709\u53d8\u5f02\u4f4d\u70b9\u7684\u6bd4\u5bf9\u6587\u4ef6\uff0c\u4e0d\u4ec5\u4ec5\u662f\u6838\u5fc3\u57fa\u56e0\u7ec4\u90e8\u5206\u3002\u8be6\u7ec6\u5c55\u793a\u4e86\u6bcf\u4e2a\u6837\u672c\u4e2d\u53d8\u5f02\u4f4d\u70b9\u7684\u4fe1\u606f\u3002<\/p>\n\n\n\n

    core.tab<\/strong>\uff1a\u4e00\u4e2a\u8868\u683c\u6587\u4ef6\uff0c\u8be6\u7ec6\u5217\u51fa\u4e86\u6240\u6709\u53d8\u5f02\u4f4d\u70b9\u53ca\u5176\u5728\u5404\u4e2a\u6837\u672c\u4e2d\u7684\u72b6\u6001\u3002\u8be5\u8868\u683c\u53ef\u4ee5\u7528\u4e8e\u8fdb\u4e00\u6b65\u7684\u7edf\u8ba1\u5206\u6790\u548c\u53d8\u5f02\u6ce8\u91ca\u3002<\/p>\n\n\n\n

    core.vcf<\/strong>\uff1a\u53d8\u5f02\u4f4d\u70b9\u7684 VCF\uff08Variant Call Format\uff09\u683c\u5f0f\u6587\u4ef6\uff0c\u5e7f\u6cdb\u7528\u4e8e\u5b58\u50a8\u57fa\u56e0\u7ec4\u53d8\u5f02\u4fe1\u606f\u3002<\/p>\n\n\n\n

    \u8be5\u6587\u4ef6\u53ef\u4ee5\u4e0e\u5176\u4ed6\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\u517c\u5bb9\uff0c\u7528\u4e8e\u8fdb\u4e00\u6b65\u7684\u53d8\u5f02\u5206\u6790\u3002<\/p>\n\n\n\n

    \u63a5\u4e0b\u6765\u6211\u4eec\u53ef\u4ee5\u5229\u7528core.aln\u8fdb\u884c\u5168\u57fa\u56e0\u7ec4SNP\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\uff0c\u5229\u7528\u6211\u4eec\u4e0a\u671f\u5206\u4eab\u8fc7\u7684IQTree2\u6d41\u7a0b\u8fdb\u884c\u8fdb\u5316\u6811\u6784\u5efa\u3002\u5982\u679c\u60f3\u8981\u627e\u6700\u4f73\u6a21\u578b\uff0c\u53ef\u4ee5\u7528-m MF\u53c2\u6570\uff0c\u8fd9\u91cc\u7528\u7684\u662fGTR\u6a21\u578b\uff0c\u7ed3\u679c\u5927\u5dee\u4e0d\u5dee\u3002<\/p>\n\n\n\n

    $ perl mfa2phy.pl core.aln core.aln.phy<\/strong><\/strong><\/p>\n\n\n\n

    $ nohup iqtree2 -s core.aln.phy -m GTR -bb 1000 -T AUTO &<\/strong><\/strong><\/p>\n\n\n\n

    \u7136\u540e\u540e\u518d\u5c06treefile\u6587\u4ef6\u653e\u5230\u8fdb\u5316\u6811\u7f8e\u5316\u8f6f\u4ef6\u5c31\u53ef\u4ee5\u770b\u5230\u7ed3\u679c\u5566\uff0c\u8fd9\u91cc\u5bfc\u5165\u7684\u662f\u5728\u7ebf\u7f51\u7ad9iTOL\uff0c\u6211\u4eec\u4e5f\u53ef\u4ee5\u7ed3\u5408\u6750\u6599\u80cc\u666f\u4fe1\u606f\u8fdb\u884c\u7f8e\u5316\u3002<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe8 \u5168\u57fa\u56e0\u7ec4SNP\u8fdb\u5316\u6811<\/p>\n\n\n\n

    3\u3001Snippy-dist\uff1acore SNP\u7cfb\u7edf\u53d1\u80b2\u5206\u6790<\/p>\n\n\n\n

    \u5f53\u6211\u4eec\u5206\u6790\u9662\u5185\u611f\u67d3\uff0c\u83cc\u682a\u4f20\u64ad\u5173\u7cfb\u7684\u65f6\u5019\u3002\u4f20\u7edf\u6700\u5e38\u7528\u7684\u65b9\u6cd5\u670916SRNA\uff0cMLST,cgMLST\uff0c\u4ee5\u53ca\u5168\u57fa\u56e0\u7ec4\u7684\u5206\u6790\uff0c\u5206\u8fa8\u7387\u4f9d\u6b21\u5347\u9ad8\u3002\u4eca\u5929snp\u5dee\u5f02\u6570\u5c31\u662f\u57fa\u4e8e\u5168\u57fa\u56e0\u7ec4\u5206\u6790\u5f97\u5230\u7684\u6700\u9ad8\u7cbe\u5ea6\u7684\u83cc\u682a\u4f20\u64ad\u5173\u7cfb\u4e4b\u95f4\u7684\u8bc1\u636e\u3002\u9996\u5148\u5bf9\u81ea\u5df1\u7684\u83cc\u682a\u7684\u591a\u4e2a\u57fa\u56e0\u7ec4\u8fdb\u884c\u6bd4\u5bf9\u751f\u6210.aln\u7ed3\u5c3e\u7684\u6587\u4ef6\uff0c\u7136\u540e\u5c31\u53ef\u4ee5\u8ba1\u7b97snp\u5dee\u5f02\u4e86\u3002\u4e0d\u540c\u7684\u83cc\u682a\u9608\u503c\u4e0d\u540c\uff0c\u5bf9\u4e8e\u4e00\u822c\u7ec6\u83cc\u83cc\u800c\u8a00SNP<40\u4e2a\u88ab\u8ba4\u4e3a\u76f4\u63a5\u7684\u83cc\u682a\u64ad\u6563\u3002<\/p>\n\n\n\n

    $ snp-dists core.aln > core.aln.snpmatrix<\/strong><\/strong><\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe9 \u4e2d\u95f4\u5904\u7406\u8fc7\u7a0b<\/p>\n\n\n\n

    $ less core.aln.snpmatrix<\/strong><\/strong><\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe9 SNP\u77e9\u9635\u6587\u4ef6<\/p>\n\n\n\n

    \u53ef\u4ee5\u770b\u5230\u7ed3\u679c\u6587\u4ef6\u662f\u4e00\u4e2aSNP\u77e9\u9635\uff0c\u63a5\u4e0b\u6765\u6211\u4eec\u5c31\u53ef\u4ee5\u7528\u70ed\u56fe\u6765\u5c55\u793a\u5566\u3002<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u56fe10 SNP\u77e9\u9635\u70ed\u56fe\u53ef\u89c6\u5316<\/p>\n\n\n\n

    \u4ece\u8fd9\u4e2a\u77e9\u9635\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u5224\u65adcase3\u3001case2\u548ccase4\u5c5e\u4e8e\u76f4\u63a5\u4f20\u64ad\u3002<\/p>\n\n\n\n

    \u4e09\u3001\u5c0f\u7ed3<\/strong><\/strong><\/h1>\n\n\n\n
    \"\"<\/figure>\n\n\n\n

    \u56fe11 Snippy\u7684\u6838\u5fc3\u529f\u80fd<\/p>\n\n\n\n

    Snippy\u7684\u6838\u5fc3\u529f\u80fd\u89c1\u4e0a\u56fe\uff0c\u4f46\u4e4b\u6240\u4ee5\u8bf4\u662f\u7ec6\u83cc\u57fa\u56e0\u7ec4\u9057\u4f20\u5206\u6790\u795e\u5668\uff0c\u539f\u56e0\u5728\u4e8e\u8be5\u5de5\u5177\u53ef\u4ee5\u81ea\u52a8\u5224\u522b\u53d8\u5f02\uff0c\u719f\u6089\u4eba\u7c7b\u7684\u5168\u57fa\u56e0\u7ec4\/\u5168\u5916\u663e\u5b50\u7ec4”\u5bb6\u7cfb”\u4e0e”\u80bf\u7624”\u53d8\u5f02\u68c0\u6d4b\u539f\u7406\u7684\u8bfb\u8005\u4eec\uff0c\u5e94\u8be5\u80fd\u7406\u89e3\u8fd9\u4e2a\u53c2\u6570\u3002\u6b64\u53c2\u6570\u80cc\u540e\u7684\u6982\u5ff5\u662f\u4e3a\u5355\u500d\u4f53\u751f\u7269\uff08\u5373\uff1a\u7ec6\u83cc\u3001\u75c5\u6bd2\u3001\u771f\u83cc\u3001\u539f\u751f\u52a8\u7269\u7b49\u4f4e\u7b49\u751f\u7269\uff09\u7684\u9057\u4f20\u5206\u6790”\u91cf\u8eab\u5b9a\u505a”\uff0c\u5426\u5219\u5c06\u5e26\u6765\u7edf\u8ba1\u5b66\u548c\u9057\u4f20\u5b66\u4e0a\u7684\u9ebb\u70e6\uff08GATK\u7684\u57fa\u56e0\u578b\u3001Mutect2-GATK\u7684\u7a81\u53d8\u8d1f\u8377\u7b49\u7edf\u8ba1\u6982\u5ff5\u4e0e\u65b9\u6cd5\uff0c\u5728\u6b64\u5904\u5747\u4e0d\u9002\u7528\uff09\uff0c\u4ee5\u4e8c\u500d\u4f53\u751f\u7269\u4e3a\u4f8b\uff0c\u8fd8\u8981\u9700\u8981\u8fdb\u884c\u6742\u5408\u63a8\u65ad\uff0c\u800c\u5bf9\u4e8e\u5355\u500d\u4f53\u751f\u7269\u6765\u8bf4\uff0c\u4e0d\u5e94\u8be5\u5b58\u5728\u6742\u5408\u5b50\uff0c\u4e5f\u65e0\u201c\u7a81\u53d8\u8d1f\u8377\u201d\u3002<\/p>\n\n\n\n

    \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

    \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\uff0c\u4e0a\u9762\u7684\u8fdb\u5316\u6811\u3001\u70ed\u56fe\u4e5f\u53ef\u4ee5\u8f7b\u677e\u7ed8\u5236\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><\/p>\n","protected":false},"excerpt":{"rendered":"

    \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\u524d\u9762\u51e0\u5929\u5728\u5916\u7f51\u4e0a\u770b\u5230\u4e00\u4e2a\u9488\u5bf9\u7ec6\u83cc\u57fa\u56e0\u7ec4SNP\u9274\u5b9a\u5de5\u5177\u7684\u8c03 […]<\/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\/61804"}],"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=61804"}],"version-history":[{"count":2,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61804\/revisions"}],"predecessor-version":[{"id":61822,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61804\/revisions\/61822"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61804"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61804"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61804"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}