{"id":72861,"date":"2026-11-15T11:49:28","date_gmt":"2026-11-15T03:49:28","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=72861"},"modified":"2026-11-15T11:51:35","modified_gmt":"2026-11-15T03:51:35","slug":"gubbins-full-alignment-snp-density-coordinate-practice","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/gubbins-full-alignment-snp-density-coordinate-practice\/","title":{"rendered":"Gubbins \u5b9e\u8dd1\u6559\u7a0b\uff5c\u4e3a\u4ec0\u4e48\u5fc5\u987b\u4fdd\u7559\u5168\u957f\u6bd4\u5bf9\u5750\u6807\uff0cSNP \u77e9\u9635\u8dd1\u901a\u4e86\u4e5f\u53ef\u80fd\u6ca1\u6709\u610f\u4e49"},"content":{"rendered":"
\n

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Gubbins \u5224\u65ad\u7684\u662f\u5c40\u90e8\u66ff\u6362\u5bc6\u5ea6\u5f02\u5e38<\/h2>\n

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IMAGE=quay.io\/biocontainers\/gubbins:3.4.3--py310hfc0ef84_1\r\ndocker pull "$IMAGE"\r\nmkdir -p numba-cache\r\n\r\ndocker run --rm --cpus 2 --memory 6g \\\r\n  -u "$(id -u):$(id -g)" -w \/work \\\r\n  -e NUMBA_CACHE_DIR=\/work\/numba-cache \\\r\n  -e NUMBA_NUM_THREADS=2 -e OMP_NUM_THREADS=2 \\\r\n  -e OPENBLAS_NUM_THREADS=2 \\\r\n  -v "$(pwd):\/work" "$IMAGE" \\\r\n  run_gubbins.py --prefix result --threads 2 \\\r\n  --tree-builder fasttree --model-fitter fasttree \\\r\n  --iterations 5 --seed 133 input.aln\r\n<\/code><\/pre>\n
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\n\n\n\n\n\n\n\n
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\u96c6\u4e2d\u7ec4<\/td>\n50000<\/td>\n380<\/td>\n1<\/td>\n200<\/td>\n<\/tr>\n
\u5206\u6563\u7ec4<\/td>\n50000<\/td>\n380<\/td>\n0<\/td>\n380<\/td>\n<\/tr>\n
\u9519\u8bef SNP \u8f93\u5165<\/td>\n380<\/td>\n380<\/td>\n2<\/td>\n218<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u96c6\u4e2d\u7ec4\u8fc7\u6ee4\u540e\u7684\u591a\u6001\u6bd4\u5bf9\u5269\u4e24\u767e\u5217\uff0c\u4e0e\u672c\u6b21\u8bbe\u8ba1\u7684\u80cc\u666f\u4f4d\u70b9\u6570\u91cf\u4e00\u81f4\u3002\u8fd9\u91cc\u8bf4\u7684\u662f\u8fc7\u6ee4\u540e\u7684\u591a\u6001\u4f4d\u70b9\u77e9\u9635\u957f\u5ea6\uff0c\u5e76\u4e0d\u662f\u58f0\u79f0\u6574\u4e2a\u57fa\u56e0\u7ec4\u53ea\u5269\u4e24\u767e\u4e2a\u78b1\u57fa\u3002\u82e5\u5728\u62a5\u544a\u4e2d\u53ea\u5199\u201c\u5e8f\u5217\u7531\u4e94\u4e07\u7f29\u77ed\u5230\u4e24\u767e\u201d\uff0c\u5c31\u4f1a\u6df7\u6dc6\u5168\u957f\u6bd4\u5bf9\u4e0e\u591a\u6001\u4f4d\u70b9\u8f93\u51fa\u4e24\u79cd\u6587\u4ef6\u3002<\/p>\n
\u5019\u9009\u533a\u95f4\u4e5f\u4e0d\u5fc5\u4e0e\u8bbe\u8ba1\u65f6\u5141\u8bb8\u653e\u7f6e\u66ff\u6362\u7684\u6574\u4e2a\u4e24\u5343\u78b1\u57fa\u7a97\u53e3\u7aef\u70b9\u5b8c\u5168\u4e00\u81f4\u3002\u8bbe\u8ba1\u7a97\u53e3\u89c4\u5b9a\u7684\u662f\u65b0\u589e\u53d8\u5f02\u53ef\u4ee5\u51fa\u73b0\u7684\u4f4d\u7f6e\uff0c\u800c\u7a0b\u5e8f\u8f93\u51fa\u8fb9\u754c\u6765\u81ea\u5b9e\u9645\u53d8\u5f02\u5206\u5e03\u4e0e\u5224\u65ad\u89c4\u5219\u3002\u672c\u6b21\u533a\u95f4\u7ed3\u675f\u4e8e\u7b2c\u4e00\u4e07\u4e00\u5343\u4e5d\u767e\u516b\u5341\u4e03\u4f4d\uff0c\u56e0\u6b64\u5e94\u539f\u6837\u62a5\u544a\uff0c\u4e0d\u5e94\u4e3a\u4e86\u8ba9\u7ed3\u679c\u6574\u9f50\u800c\u624b\u5de5\u6539\u6210\u7b2c\u4e00\u4e07\u4e8c\u5343\u3002<\/p>\n
\u9519\u8bef\u7684 SNP \u8f93\u5165\u4ecd\u7136\u6210\u529f\u7ed3\u675f<\/h2>\n
\u4ec5\u4fdd\u7559 SNP \u5217\u7684\u7b2c\u4e09\u7ec4\u9000\u51fa\u7801\u540c\u6837\u4e3a\u96f6\uff0c\u5e76\u8f93\u51fa\u4e24\u4e2a\u5019\u9009\u533a\u57df\u3002\u5176\u4e2d\u4e00\u4e2a\u4f4d\u4e8e\u538b\u7f29\u540e\u5750\u6807 55\u2013212\uff0c\u5173\u8054 S1 \u548c S2\uff0c\u8bb0\u5f55\u4e00\u767e\u4e94\u5341\u516b\u4e2a\u66ff\u6362\u3002\u53e6\u4e00\u4e2a\u4f4d\u4e8e 272\u2013278\uff0c\u5173\u8054 S7 \u548c S8\uff0c\u8bb0\u5f55\u56db\u4e2a\u66ff\u6362\u3002\u8fc7\u6ee4\u540e\u4fdd\u7559\u4e8c\u767e\u4e00\u5341\u516b\u5217\uff0c\u5df2\u7ecf\u4e0d\u540c\u4e8e\u6b63\u786e\u5168\u957f\u8f93\u5165\u7684\u4e24\u767e\u5217\u3002<\/p>\n
\u8fd9\u4e9b\u5750\u6807\u662f\u4e09\u767e\u516b\u5341\u5217\u538b\u7f29\u77e9\u9635\u4e2d\u7684\u4f4d\u7f6e\uff0c\u4e0d\u80fd\u76f4\u63a5\u5f53\u6210\u539f\u4e94\u4e07\u78b1\u57fa\u5e8f\u5217\u4e0a\u7684\u5750\u6807\u3002\u5373\u4fbf\u53e6\u5916\u4fdd\u5b58\u4e86\u5217\u5230\u539f\u59cb\u4f4d\u7f6e\u7684\u6620\u5c04\uff0c\u4e5f\u4e0d\u80fd\u7b80\u5355\u6620\u5c04\u56de\u53bb\u540e\u5c31\u628a\u7ed3\u679c\u5f53\u4f5c\u6b63\u786e\u63a8\u65ad\uff0c\u56e0\u4e3a\u7b97\u6cd5\u8ba1\u7b97\u5c40\u90e8\u5bc6\u5ea6\u65f6\u4f7f\u7528\u7684\u95f4\u9694\u5df2\u7ecf\u6539\u53d8\u3002\u5750\u6807\u89e3\u91ca\u9519\u8bef\u548c\u7edf\u8ba1\u8f93\u5165\u9519\u8bef\u662f\u540c\u65f6\u53d1\u751f\u7684\u3002<\/p>\n
\u8fd9\u6b21\u8fd0\u884c\u6700\u6709\u4ef7\u503c\u7684\u73b0\u8c61\u4e0d\u662f\u201c\u9519\u683c\u5f0f\u4f1a\u62a5\u9519\u201d\uff0c\u800c\u662f\u683c\u5f0f\u6709\u6548\u3001\u524d\u63d0\u65e0\u6548\u7684\u8f93\u5165\u53ef\u80fd\u7167\u5e38\u4ea7\u751f\u6574\u5957\u7ed3\u679c\u3002\u7a0b\u5e8f\u80fd\u9a8c\u8bc1\u5b57\u7b26\u548c\u957f\u5ea6\uff0c\u5374\u4e0d\u80fd\u4ece\u4e00\u4e2a\u770b\u8d77\u6765\u6574\u9f50\u7684\u77e9\u9635\u4e2d\u77e5\u9053\u4e2d\u95f4\u66fe\u7ecf\u5220\u6389\u56db\u4e07\u591a\u5217\u3002\u5206\u6790\u8005\u5fc5\u987b\u5728\u8fdb\u5165\u6d41\u7a0b\u524d\u6838\u5b9e\u6bd4\u5bf9\u662f\u600e\u6837\u6784\u5efa\u7684\u3002<\/p>\n
\u56e0\u6b64\uff0c\u4e0d\u5e94\u628a\u8f93\u51fa\u6811\u5b58\u5728\u3001\u533a\u57df\u6587\u4ef6\u4e0d\u4e3a\u7a7a\u3001\u7a0b\u5e8f\u6ca1\u6709\u5f02\u5e38\u89c6\u4e3a\u65b9\u6cd5\u9002\u7528\u6027\u7684\u5145\u5206\u8bc1\u636e\u3002\u4e00\u6b21\u5b8c\u6574\u7684\u5206\u6790\u5ba1\u67e5\uff0c\u9700\u8981\u540c\u65f6\u68c0\u67e5\u8f93\u5165\u6765\u6e90\u3001\u5750\u6807\u4fdd\u7559\u65b9\u5f0f\u3001\u6837\u672c\u8303\u56f4\u548c\u8f93\u51fa\u89e3\u91ca\u3002\u81ea\u52a8\u5316\u6d41\u7a0b\u53ef\u4ee5\u68c0\u67e5\u5176\u4e2d\u4e00\u90e8\u5206\uff0c\u4f46\u4ecd\u8981\u628a\u8fd9\u4e9b\u524d\u63d0\u5199\u5165\u5206\u6790\u8bb0\u5f55\u3002<\/p>\n
\u4ece Snippy \u8854\u63a5\u65f6\u5e94\u8be5\u9009\u54ea\u4e2a\u6587\u4ef6<\/h2>\n
\u5982\u679c\u4e0a\u6e38\u4f7f\u7528 Snippy\uff0c\u5173\u952e\u662f\u533a\u5206\u6838\u5fc3 SNP \u6bd4\u5bf9\u4e0e\u6838\u5fc3\u5168\u957f\u6bd4\u5bf9\u3002\u524d\u8005\u53ea\u4fdd\u7559\u5171\u540c\u53ef\u6bd4\u8f83\u7684\u591a\u6001\u5217\uff0c\u9002\u5408\u67d0\u4e9b\u8ddd\u79bb\u548c\u6784\u6811\u4efb\u52a1\uff0c\u4f46\u5df2\u7ecf\u538b\u7f29\u4e86\u7a7a\u95f4\u4fe1\u606f\u3002\u540e\u8005\u4fdd\u7559\u53c2\u8003\u5750\u6807\u8303\u56f4\u53ca\u7f3a\u5931\u5b57\u7b26\uff0c\u7ecf\u8fc7\u9002\u5f53\u6e05\u7406\u540e\uff0c\u624d\u4fdd\u6709\u672c\u7c7b\u5206\u6790\u6240\u9700\u7684\u4f4d\u7f6e\u5173\u7cfb\u3002<\/p>\n
snippy-clean_full_aln core.full.aln > clean.full.aln\r\nrun_gubbins.py --prefix lineage --threads 2 clean.full.aln\r\n<\/code><\/pre>\n
\u6e05\u7406\u5b57\u7b26\u4e0d\u7b49\u4e8e\u5220\u9664\u5217\u3002\u8fd0\u884c\u540e\u5e94\u6838\u5bf9\u5404\u5e8f\u5217\u957f\u5ea6\u4e00\u81f4\u3001\u6807\u9898\u552f\u4e00\u3001\u5b57\u7b26\u96c6\u5408\u7b26\u5408\u8981\u6c42\uff0c\u5e76\u786e\u8ba4\u5168\u957f\u957f\u5ea6\u4e0e\u53c2\u8003\u5750\u6807\u7ea6\u5b9a\u76f8\u7b26\u3002\u82e5\u8f93\u5165\u6765\u81ea\u62fc\u63a5\u7684\u591a\u4e2a\u7247\u6bb5\uff0c\u8fd8\u8981\u4fdd\u7559\u7247\u6bb5\u8fb9\u754c\u4e0e\u5750\u6807\u6620\u5c04\uff0c\u907f\u514d\u628a\u4eba\u4e3a\u76f8\u90bb\u7684\u533a\u57df\u89e3\u91ca\u4e3a\u57fa\u56e0\u7ec4\u4e0a\u7684\u771f\u5b9e\u90bb\u63a5\u3002<\/p>\n
\u540c\u6837\uff0c\u6cdb\u57fa\u56e0\u7ec4\u8f6f\u4ef6\u8f93\u51fa\u7684\u6838\u5fc3\u57fa\u56e0\u4e32\u8054\u5e8f\u5217\u867d\u7136\u5e38\u88ab\u7528\u4e8e\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\uff0c\u4e5f\u4e0d\u80fd\u56e0\u4e3a\u5b83\u53eb core alignment \u5c31\u76f4\u63a5\u62ff\u6765\u8fd0\u884c\u3002\u57fa\u56e0\u987a\u5e8f\u3001\u95f4\u9694\u4ee5\u53ca\u4e0d\u5728\u6838\u5fc3\u96c6\u5408\u4e2d\u7684\u533a\u57df\u53ef\u80fd\u5df2\u7ecf\u53d1\u751f\u6539\u53d8\u3002\u9009\u62e9\u8f93\u5165\u8981\u6839\u636e\u65b9\u6cd5\u9700\u8981\u7684\u4fe1\u606f\uff0c\u800c\u4e0d\u662f\u6839\u636e\u6587\u4ef6\u540d\u4e2d\u7684\u201c\u6838\u5fc3\u201d\u4e8c\u5b57\u3002<\/p>\n
\u9000\u51fa\u6210\u529f\u4ee5\u540e\u8fd8\u8981\u770b\u505c\u6b62\u539f\u56e0<\/h2>\n
\u672c\u6b21\u4e09\u7ec4\u6700\u7ec8\u90fd\u8fbe\u5230\u8bbe\u5b9a\u7684\u4e94\u8f6e\u4e0a\u9650\u540e\u505c\u6b62\uff0c\u65e5\u5fd7\u6ca1\u6709\u8bc1\u660e\u5df2\u7ecf\u6309\u6536\u655b\u6807\u51c6\u7ed3\u675f\u3002\u56e0\u6b64\u672c\u6587\u62a5\u544a\u7684\u662f\u8be5\u660e\u786e\u8fed\u4ee3\u8bbe\u7f6e\u4e0b\u7684\u8f93\u51fa\uff0c\u4e0d\u80fd\u63cf\u8ff0\u6210\u5df2\u7ecf\u83b7\u5f97\u7a33\u5b9a\u6536\u655b\u7684\u6700\u7ec8\u7cfb\u7edf\u53d1\u80b2\u5173\u7cfb\u3002\u6b64\u524d\u4e09\u8f6e\u8bd5\u8dd1\u7528\u4e8e\u68c0\u67e5\u6d41\u7a0b\uff0c\u6b63\u5f0f\u590d\u73b0\u5305\u4fdd\u5b58\u4e94\u8f6e\u8fd0\u884c\u7ed3\u679c\u3002<\/p>\n
\u5bf9\u771f\u5b9e\u9879\u76ee\u800c\u8a00\uff0c\u8fbe\u5230\u4e0a\u9650\u548c\u6ee1\u8db3\u6536\u655b\u6761\u4ef6\u9700\u8981\u533a\u522b\u8bb0\u5f55\u3002\u5982\u679c\u7814\u7a76\u7ed3\u8bba\u4f9d\u8d56\u6811\u62d3\u6251\u6216\u67d0\u4e9b\u8fb9\u754c\uff0c\u5e94\u7ee7\u7eed\u68c0\u67e5\u8fed\u4ee3\u53d8\u5316\uff0c\u5224\u65ad\u662f\u5426\u9700\u8981\u66f4\u5408\u9002\u7684\u6837\u672c\u5206\u7ec4\u3001\u6a21\u578b\u6216\u8fed\u4ee3\u8bbe\u7f6e\u3002\u4e0d\u80fd\u53ea\u628a\u4e0a\u9650\u968f\u610f\u8c03\u5927\uff0c\u7136\u540e\u5047\u5b9a\u6240\u6709\u4e0d\u7a33\u5b9a\u6027\u90fd\u4f1a\u6d88\u5931\u3002<\/p>\n
\u540c\u6837\uff0c\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\u4e3b\u8981\u5e2e\u52a9\u590d\u73b0\u968f\u673a\u8fc7\u7a0b\uff0c\u5e76\u4e0d\u4fdd\u8bc1\u6362\u4e86\u8f6f\u4ef6\u6784\u5efa\u3001\u4f9d\u8d56\u6216\u6570\u636e\u987a\u5e8f\u540e\u6240\u6709\u5185\u90e8\u8282\u70b9\u7f16\u53f7\u90fd\u4fdd\u6301\u4e00\u81f4\u3002\u5ba1\u6838\u65f6\u66f4\u5e94\u8be5\u6838\u5bf9\u533a\u57df\u5750\u6807\u3001\u5173\u8054\u53f6\u8282\u70b9\u3001\u4f4d\u70b9\u6570\u91cf\u548c\u4e3b\u8981\u5173\u7cfb\uff0c\u800c\u4e0d\u662f\u53ea\u6bd4\u8f83\u6811\u6587\u4ef6\u4e2d\u7684\u5185\u90e8\u7f16\u53f7\u5b57\u7b26\u4e32\u3002<\/p>\n
\u5982\u4f55\u628a\u5019\u9009\u533a\u57df\u53d8\u6210\u503c\u5f97\u76f8\u4fe1\u7684\u7ed3\u679c<\/h2>\n
\u5148\u68c0\u67e5\u5019\u9009\u533a\u57df\u7684\u539f\u59cb\u8bc1\u636e\u3002\u82e5\u5b83\u4f4d\u4e8e\u8986\u76d6\u5f02\u5e38\u6216\u6bd4\u5bf9\u8d28\u91cf\u660e\u663e\u4e0b\u964d\u7684\u4f4d\u7f6e\uff0c\u5e94\u4f18\u5148\u6392\u67e5\u6570\u636e\u95ee\u9898\u3002\u82e5\u533a\u57df\u53ea\u5728\u5c11\u6570\u4f4e\u8d28\u91cf\u6837\u672c\u4e2d\u51fa\u73b0\uff0c\u4e5f\u5e94\u68c0\u67e5\u7f3a\u5931\u6a21\u5f0f\u662f\u5426\u5f71\u54cd\u63a8\u65ad\u3002\u533a\u57df\u56fe\u53ef\u4ee5\u5e2e\u52a9\u5b9a\u4f4d\u95ee\u9898\uff0c\u4f46\u4e0d\u80fd\u4ee3\u66ff\u8bfb\u6bb5\u548c\u6bd4\u5bf9\u672c\u8eab\u3002<\/p>\n
\u518d\u68c0\u67e5\u6837\u672c\u7fa4\u4f53\u662f\u5426\u8fc7\u4e8e\u5206\u6563\u3002\u5c06\u5dee\u5f02\u5f88\u5927\u7684\u591a\u4e2a\u8c31\u7cfb\u653e\u8fdb\u540c\u4e00\u6b21\u5206\u6790\uff0c\u53ef\u80fd\u6539\u53d8\u80cc\u666f\u66ff\u6362\u6c34\u5e73\u53ca\u5c40\u90e8\u5f02\u5e38\u7684\u89e3\u91ca\u3002\u5b98\u65b9\u624b\u518c\u5efa\u8bae\u5728\u5408\u9002\u7684\u8fd1\u7f18\u7fa4\u4f53\u8303\u56f4\u5185\u4f7f\u7528\uff0c\u5e76\u8ba8\u8bba\u4e86\u6f5c\u5728\u6df7\u6742\u56e0\u7d20\u3002Gubbins \u4f7f\u7528\u624b\u518c<\/a><\/p>\n
\u6700\u540e\u68c0\u67e5\u5750\u6807\u80fd\u5426\u7a33\u5b9a\u56de\u5230\u53c2\u8003\u4e0e\u6ce8\u91ca\u3002\u533a\u57df\u6587\u4ef6\u63cf\u8ff0\u7684\u662f\u6bd4\u5bf9\u4e0a\u7684\u533a\u95f4\uff0c\u53e0\u52a0\u57fa\u56e0\u529f\u80fd\u65f6\u8fd8\u9700\u8981\u660e\u786e\u5750\u6807\u7cfb\u7edf\u3002\u82e5\u53c2\u8003\u6765\u81ea\u591a\u6761 contig \u6216\u7ecf\u8fc7\u91cd\u6392\uff0c\u4e0d\u5e94\u628a\u533a\u95f4\u6570\u5b57\u76f4\u63a5\u5bf9\u7167\u53e6\u4e00\u4efd\u672a\u7ecf\u6620\u5c04\u7684\u6ce8\u91ca\u6587\u4ef6\u3002\u5f88\u591a\u770b\u8d77\u6765\u50cf\u751f\u7269\u5b66\u89e3\u91ca\u7684\u95ee\u9898\uff0c\u5176\u5b9e\u6765\u81ea\u5750\u6807\u5bf9\u8c61\u4e0d\u4e00\u81f4\u3002<\/p>\n
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