{"id":72859,"date":"2026-11-15T11:49:27","date_gmt":"2026-11-15T03:49:27","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=72859"},"modified":"2026-11-15T11:51:32","modified_gmt":"2026-11-15T03:51:32","slug":"snippy-low-coverage-consensus-core-alignment-practice","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/snippy-low-coverage-consensus-core-alignment-practice\/","title":{"rendered":"Snippy \u5b9e\u8dd1\u6559\u7a0b\uff5c\u5c11\u68c0\u51fa\u4e00\u4e2a SNP\uff0c\u53ef\u80fd\u53ea\u662f\u8986\u76d6\u4e0d\u8db3\uff0c\u600e\u6837\u907f\u514d\u5171\u8bc6\u5e8f\u5217\u5236\u9020\u5047\u4e00\u81f4"},"content":{"rendered":"
\n

\u540c\u4e00\u6761\u7ec6\u83cc\u5e8f\u5217\uff0c\u6539\u53d8\u6d4b\u5e8f\u8986\u76d6\u540e\uff0c\u53d8\u5f02\u8868\u91cc\u7684 SNP \u6570\u91cf\u4f1a\u4e0d\u4f1a\u53d8\u5316\u3002\u7b54\u6848\u901a\u5e38\u5bb9\u6613\u60f3\u5230\uff0c\u4f46\u771f\u6b63\u5bb9\u6613\u51fa\u9519\u7684\u662f\u4e0b\u4e00\u6b65\u3002\u5206\u6790\u8005\u628a\u53d8\u5f02\u8868\u5e94\u7528\u5230\u53c2\u8003\u4e0a\u751f\u6210\u5171\u8bc6\u5e8f\u5217\uff0c\u518d\u628a\u6ca1\u6709\u53d8\u5316\u7684\u4f4d\u7f6e\u90fd\u5f53\u4f5c\u771f\u5b9e\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u3002\u8fd9\u6837\u4e00\u6765\uff0c\u6570\u636e\u4e0d\u8db3\u5c31\u53ef\u80fd\u88ab\u5305\u88c5\u6210\u5e8f\u5217\u4e00\u81f4\u3002<\/p>\n

\u672c\u7bc7\u5b9e\u9645\u5b89\u88c5 Snippy 4.6.0\uff0c\u7528\u540c\u4e00\u4e2a\u5df2\u77e5\u5e8f\u5217\u771f\u503c\u751f\u6210\u4e09\u7ec4\u8bfb\u6bb5\uff0c\u5206\u522b\u4fdd\u7559\u6b63\u5e38\u8986\u76d6\u3001\u6316\u53bb\u4e00\u4e2a\u8986\u76d6\u533a\u95f4\uff0c\u4ee5\u53ca\u5728\u8be5\u533a\u95f4\u8865\u56de\u5c11\u91cf\u8bfb\u6bb5\u3002\u6211\u4eec\u6cbf\u7740\u53d8\u5f02\u8868\u3001\u6bd4\u5bf9\u5e8f\u5217\u3001\u5171\u8bc6\u5e8f\u5217\u548c\u591a\u6837\u672c\u6838\u5fc3\u6bd4\u5bf9\u9010\u5c42\u68c0\u67e5\uff0c\u770b\u770b\u4e00\u4e2a\u4f4d\u70b9\u4e3a\u4ec0\u4e48\u4f1a\u53d8\u6210\u66ff\u4ee3\u78b1\u57fa\u3001\u7f3a\u53e3\u6216\u672a\u77e5\u5b57\u7b26\u3002<\/p>\n

\"\u672a\u68c0\u51fa
\u540c\u4e00\u5e8f\u5217\u771f\u503c\uff0c\u4e09\u79cd\u8986\u76d6\u6761\u4ef6<\/figcaption><\/figure>\n

\u5148\u770b\u8f93\u5165\u6761\u4ef6\uff0c\u518d\u51b3\u5b9a\u80fd\u5426\u4f7f\u7528\u8fd9\u7c7b\u6d41\u7a0b<\/h2>\n

Snippy \u9762\u5411\u5355\u500d\u4f53\u53d8\u5f02\u5206\u6790\uff0c\u5e38\u7528\u4e8e\u7ec6\u83cc\u5206\u79bb\u682a\u8bfb\u6bb5\u76f8\u5bf9\u53c2\u8003\u7684\u6bd4\u8f83\u3002\u5b83\u6574\u5408\u8bfb\u6bb5\u6bd4\u5bf9\u3001\u53d8\u5f02\u8c03\u7528\u53ca\u7ed3\u679c\u6574\u7406\uff0c\u8ba9\u591a\u4e2a\u6837\u672c\u53ef\u4ee5\u8fdb\u5165\u4e00\u81f4\u7684\u5206\u6790\u6d41\u7a0b\u3002\u5b98\u65b9\u4ed3\u5e93<\/a>\u63d0\u4f9b\u8f93\u5165\u683c\u5f0f\u3001\u7ed3\u679c\u6587\u4ef6\u548c\u6838\u5fc3\u6bd4\u5bf9\u8bf4\u660e\u3002\u5b83\u7684\u4fbf\u5229\u4e4b\u5904\u662f\u51cf\u5c11\u624b\u5de5\u62fc\u63a5\u6b65\u9aa4\uff0c\u4f46\u4e0d\u4f1a\u66ff\u5206\u6790\u8005\u51b3\u5b9a\u53c2\u8003\u662f\u5426\u5408\u9002\u3001\u6837\u672c\u662f\u5426\u6df7\u5408\uff0c\u4ee5\u53ca\u7f3a\u5931\u8bc1\u636e\u5e94\u8be5\u600e\u6837\u8fdb\u5165\u4e0b\u6e38\u7edf\u8ba1\u3002<\/p>\n

\u53c2\u8003\u9009\u62e9\u76f4\u63a5\u51b3\u5b9a\u54ea\u4e9b\u4f4d\u7f6e\u6709\u673a\u4f1a\u88ab\u53ef\u9760\u6bd4\u8f83\u3002\u82e5\u53c2\u8003\u4e0e\u6837\u672c\u5dee\u5f02\u8f83\u5927\uff0c\u4e00\u4e9b\u533a\u57df\u53ef\u80fd\u65e0\u6cd5\u6b63\u5e38\u6bd4\u5bf9\uff0c\u8f93\u51fa\u4e2d\u7f3a\u5931\u4f4d\u7f6e\u589e\u52a0\u3002\u8fd9\u65f6\u53ea\u770b\u68c0\u51fa\u7684 SNP \u603b\u6570\uff0c\u53ef\u80fd\u5f97\u5230\u76f8\u53cd\u7684\u5370\u8c61\uff0c\u56e0\u4e3a\u8bb8\u591a\u672c\u5e94\u8ba8\u8bba\u7684\u4f4d\u7f6e\u6839\u672c\u6ca1\u6709\u901a\u8fc7\u5206\u6790\u6761\u4ef6\u3002\u771f\u5b9e\u9879\u76ee\u4e2d\uff0c\u5e94\u5148\u9605\u8bfb\u8986\u76d6\u3001\u53ef\u6bd4\u5bf9\u957f\u5ea6\u548c\u8d28\u91cf\uff0c\u518d\u89e3\u91ca\u53d8\u5f02\u6570\u91cf\u3002<\/p>\n

\u672c\u6b21\u523b\u610f\u4f7f\u7528\u540c\u4e00\u53c2\u8003\u7247\u6bb5\u53ca\u5176\u786e\u5b9a\u7684\u66ff\u6362\uff0c\u6392\u9664\u4e86\u590d\u6742\u53c2\u8003\u5dee\u5f02\uff0c\u4e5f\u6ca1\u6709\u5f15\u5165\u6d4b\u5e8f\u9519\u8bef\u3001\u6df7\u5408\u83cc\u682a\u548c\u7ed3\u6784\u53d8\u5f02\u3002\u8fd9\u79cd\u7b80\u5316\u9002\u5408\u9a8c\u8bc1\u6587\u4ef6\u8bed\u4e49\uff0c\u4e0d\u4ee3\u8868\u5b9e\u9645\u6837\u672c\u4e5f\u4f1a\u50cf\u793a\u4f8b\u4e00\u6837\u5e72\u51c0\u3002\u6587\u7ae0\u540e\u9762\u7684\u89c2\u5bdf\u53ea\u5bf9\u672c\u6b21\u6761\u4ef6\u6210\u7acb\uff0c\u4e0d\u7528\u4e8e\u5ba3\u79f0\u67d0\u4e00\u8c03\u7528\u9608\u503c\u5728\u6240\u6709\u9879\u76ee\u4e2d\u6700\u4f18\u3002<\/p>\n

\u6784\u9020\u4e09\u7ec4\u53ea\u6709\u8986\u76d6\u6761\u4ef6\u4e0d\u540c\u7684\u6570\u636e<\/h2>\n

\u53c2\u8003\u6765\u81ea\u516c\u5f00\u7684\u5927\u80a0\u6746\u83cc NC_000913.3\uff0c\u53d6\u524d\u9762\u4e09\u4e07\u4e2a\u78b1\u57fa\u3002\u6211\u4eec\u5728\u4ece\u4e00\u5f00\u59cb\u8ba1\u6570\u7684\u7b2c\u4e94\u5343\u3001\u7b2c\u4e00\u4e07\u4e94\u5343\u548c\u7b2c\u4e8c\u4e07\u4e94\u5343\u4f4d\u5206\u522b\u8bbe\u7f6e\u660e\u786e\u66ff\u6362\u3002\u4e09\u7ec4\u8bfb\u6bb5\u90fd\u6765\u81ea\u8fd9\u6761\u6539\u53d8\u540e\u7684\u5e8f\u5217\uff0c\u6240\u4ee5\u4e09\u5904\u66ff\u6362\u662f\u5171\u540c\u771f\u503c\uff0c\u4e0d\u662f\u4e09\u7ec4\u6837\u672c\u4e4b\u95f4\u7684\u751f\u7269\u5b66\u5dee\u5f02\u3002<\/p>\n

\u7b2c\u4e00\u7ec4\u751f\u6210\u516b\u5343\u5bf9\u957f\u5ea6\u4e3a\u4e00\u767e\u4e94\u5341\u78b1\u57fa\u7684\u53cc\u7aef\u8bfb\u6bb5\uff0c\u7247\u6bb5\u957f\u5ea6\u5728\u4e09\u767e\u4e94\u5341\u81f3\u4e94\u767e\u4e94\u5341\u4e4b\u95f4\uff0c\u4f7f\u7528\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\uff0c\u5e76\u6392\u9664\u91cd\u590d\u7684\u8d77\u70b9\u4e0e\u957f\u5ea6\u7ec4\u5408\u3002\u7b2c\u4e8c\u7ec4\u79fb\u9664\u4e24\u7aef\u8bfb\u6bb5\u4e0e\u6307\u5b9a\u533a\u95f4\u91cd\u53e0\u7684\u7247\u6bb5\uff0c\u4f7f\u4e2d\u95f4\u76ee\u6807\u4f4d\u7f6e\u6ca1\u6709\u8986\u76d6\u3002\u7b2c\u4e09\u7ec4\u5728\u7b2c\u4e8c\u7ec4\u57fa\u7840\u4e0a\u8865\u56de\u4e09\u4e2a\u4e0d\u540c\u7247\u6bb5\uff0c\u8ba9\u76ee\u6807\u4f4d\u7f6e\u53ea\u6709\u4e09\u6761\u8bfb\u6bb5\u652f\u6301\u3002<\/p>\n

\u8fd9\u91cc\u5220\u9664\u7684\u662f\u6d4b\u5e8f\u89c2\u5bdf\uff0c\u4e0d\u662f\u628a\u76ee\u6807\u53d8\u5f02\u4ece\u6837\u672c\u57fa\u56e0\u7ec4\u4e2d\u6539\u56de\u53c2\u8003\u3002\u8fd9\u4e2a\u533a\u522b\u975e\u5e38\u5173\u952e\u3002\u53ea\u6709\u4fdd\u6301\u771f\u503c\u4e0d\u53d8\uff0c\u6211\u4eec\u624d\u80fd\u628a\u8f93\u51fa\u5dee\u5f02\u5f52\u56e0\u4e8e\u8986\u76d6\u548c\u8fc7\u6ee4\u6761\u4ef6\uff0c\u800c\u4e0d\u662f\u540c\u65f6\u6539\u53d8\u8f93\u5165\u57fa\u56e0\u578b\u9020\u6210\u65e0\u6cd5\u89e3\u91ca\u7684\u6df7\u5408\u5bf9\u7167\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u6761\u4ef6<\/th>\n\u8bfb\u6bb5\u5bf9\u6570<\/th>\n\u4f4d\u70b9 15000 \u7684\u6df1\u5ea6<\/th>\n\u53d8\u5f02\u8868 SNP \u6570<\/th>\n\u4f4d\u70b9\u771f\u503c<\/th>\n<\/tr>\n<\/thead>\n
\u6b63\u5e38\u8986\u76d6<\/td>\n8000<\/td>\n69<\/td>\n3<\/td>\nT<\/td>\n<\/tr>\n
\u65e0\u8986\u76d6<\/td>\n7313<\/td>\n0<\/td>\n2<\/td>\nT<\/td>\n<\/tr>\n
\u4f4e\u8986\u76d6<\/td>\n7316<\/td>\n3<\/td>\n2<\/td>\nT<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u6df1\u5ea6\u662f\u8fd0\u884c\u540e\u4ece BAM \u4e2d\u6309\u8d28\u91cf\u6761\u4ef6\u8bfb\u53d6\u7684\u7ed3\u679c\uff0c\u4e0d\u662f\u53ea\u6839\u636e\u751f\u6210\u8bfb\u6bb5\u6570\u91cf\u63a8\u7b97\u3002\u4e09\u7ec4\u5728\u7b2c\u4e94\u5343\u548c\u7b2c\u4e8c\u4e07\u4e94\u5343\u4f4d\u7684\u6df1\u5ea6\u5747\u5206\u522b\u4e3a\u4e03\u5341\u4e94\u548c\u516b\u5341\u4e8c\uff0c\u56e0\u800c\u8fd9\u4e24\u4e2a\u4f4d\u7f6e\u8fd8\u80fd\u7528\u6765\u786e\u8ba4\u5b9e\u9a8c\u6ca1\u6709\u987a\u4fbf\u6539\u53d8\u6240\u6709\u533a\u57df\u7684\u89c2\u5bdf\u6761\u4ef6\u3002<\/p>\n

\u5b89\u88c5\u4e0e\u8c03\u7528\u65f6\u628a\u5173\u952e\u9608\u503c\u5199\u660e<\/h2>\n

\u672c\u6b21\u56fa\u5b9a\u955c\u50cf\u4e2d\u7684 Snippy \u7248\u672c\u4e3a 4.6.0\u3002\u6bcf\u7ec4\u4f7f\u7528\u4e24\u4e2a\u7ebf\u7a0b\uff0c\u663e\u5f0f\u6307\u5b9a\u6700\u4f4e\u8986\u76d6\u5341\u548c\u53d8\u5f02\u652f\u6301\u6bd4\u4f8b\u96f6\u70b9\u4e5d\u3002\u955c\u50cf\u5b9e\u9645\u5e2e\u52a9\u4e2d\uff0c\u652f\u6301\u6bd4\u4f8b\u53c2\u6570\u7684\u9ed8\u8ba4\u503c\u4e3a\u96f6\uff0c\u8868\u793a\u81ea\u52a8\u6a21\u5f0f\u3002\u56e0\u6b64\u672c\u6587\u7684\u96f6\u70b9\u4e5d\u662f\u5b9e\u9a8c\u8bbe\u7f6e\uff0c\u4e0d\u80fd\u5199\u6210\u8f6f\u4ef6\u9ed8\u8ba4\u503c\u3002<\/p>\n

IMAGE=quay.io\/biocontainers\/snippy:4.6.0--hdfd78af_6\r\ndocker pull "$IMAGE"\r\ndocker run --rm "$IMAGE" snippy --version\r\n\r\ndocker run --rm --cpus 2 --memory 6g \\\r\n  -u "$(id -u):$(id -g)" -w \/work -v "$(pwd):\/work" "$IMAGE" \\\r\n  snippy --ref \/work\/reference.fna \\\r\n  --R1 \/work\/covered_R1.fq --R2 \/work\/covered_R2.fq \\\r\n  --outdir \/work\/covered --cpus 2 --ram 4 \\\r\n  --mincov 10 --minfrac 0.9\r\n<\/code><\/pre>\n
\u6bd4\u5bf9\u8d28\u91cf\u3001\u78b1\u57fa\u8d28\u91cf\u3001\u53d8\u5f02\u8d28\u91cf\u548c\u652f\u6301\u6bd4\u4f8b\u7ea6\u675f\u7684\u662f\u4e0d\u540c\u95ee\u9898\u3002\u8986\u76d6\u8db3\u591f\u4f46\u6bd4\u5bf9\u4e0d\u552f\u4e00\uff0c\u4e0d\u80fd\u901a\u8fc7\u589e\u52a0\u8bfb\u6bb5\u6570\u91cf\u81ea\u52a8\u89e3\u51b3\u3002\u652f\u6301\u6bd4\u4f8b\u5f88\u9ad8\u4f46\u53ea\u6709\u4e09\u6761\u8bfb\u6bb5\uff0c\u4e5f\u4e0d\u7b49\u4e8e\u6ee1\u8db3\u6700\u4f4e\u8986\u76d6\u6761\u4ef6\u3002\u9605\u8bfb\u547d\u4ee4\u65f6\uff0c\u8981\u628a\u8fd9\u4e9b\u6761\u4ef6\u770b\u4f5c\u5171\u540c\u4f5c\u7528\u7684\u4e00\u7ec4\u8fc7\u6ee4\u89c4\u5219\uff0c\u800c\u4e0d\u662f\u4e00\u4e2a\u53ef\u968f\u610f\u66ff\u6362\u7684\u8d28\u91cf\u5206\u6570\u3002<\/p>\n
\u590d\u73b0\u5b9e\u9a8c\u5305\u4f1a\u81ea\u52a8\u6784\u9020\u4e09\u7ec4\u8bfb\u6bb5\u3001\u8fd0\u884c\u4e09\u6b21\u8c03\u7528\u5e76\u6536\u96c6\u7ed3\u679c\u3002\u65b0\u9879\u76ee\u5efa\u8bae\u9009\u62e9\u7a7a\u8f93\u51fa\u76ee\u5f55\uff0c\u5e76\u8bb0\u5f55\u53c2\u8003\u6458\u8981\u3001\u8f6f\u4ef6\u7248\u672c\u548c\u53c2\u6570\u3002\u5c24\u5176\u5728\u53cd\u590d\u8c03\u53c2\u65f6\uff0c\u4e0d\u5e94\u53ea\u4fdd\u5b58\u6700\u7ec8\u90a3\u6b21\u53d8\u5f02\u8868\uff0c\u5426\u5219\u65e0\u6cd5\u89e3\u91ca\u662f\u54ea\u4e00\u6b65\u8fc7\u6ee4\u6539\u53d8\u4e86\u7ed3\u8bba\u3002<\/p>\n
\u7b2c\u4e00\u4e2a\u53d1\u73b0\uff0c\u53d8\u5f02\u8868\u7f3a\u5c11\u8bb0\u5f55\u4e0d\u7b49\u4e8e\u53c2\u8003\u4e00\u81f4<\/h2>\n
\u6b63\u5e38\u8986\u76d6\u7ec4\u5728\u4e09\u4e2a\u76ee\u6807\u4f4d\u7f6e\u90fd\u68c0\u51fa\u4e86\u9884\u671f\u66ff\u6362\u3002\u65e0\u8986\u76d6\u7ec4\u548c\u4f4e\u8986\u76d6\u7ec4\u90fd\u53ea\u4fdd\u7559\u53e6\u5916\u4e24\u4e2a\u4f4d\u7f6e\uff0c\u4e2d\u95f4\u76ee\u6807\u6ca1\u6709\u8fdb\u5165\u6700\u7ec8\u53d8\u5f02\u8868\u3002\u7531\u4e8e\u6211\u4eec\u4e8b\u5148\u77e5\u9053\u4e09\u7ec4\u771f\u503c\u76f8\u540c\uff0c\u8fd9\u4e2a\u5dee\u522b\u8bf4\u660e\u8c03\u7528\u7ed3\u679c\u4e0d\u4ec5\u53cd\u6620\u6837\u672c\u5e8f\u5217\uff0c\u4e5f\u53cd\u6620\u5f53\u524d\u8bfb\u6bb5\u662f\u5426\u63d0\u4f9b\u8db3\u591f\u8bc1\u636e\u3002<\/p>\n
\u5bf9\u4e8e\u4f4e\u8986\u76d6\u7ec4\uff0c\u4e09\u6761\u8bfb\u6bb5\u652f\u6301\u7684\u90fd\u662f\u66ff\u4ee3\u78b1\u57fa\uff0c\u4f46\u5b83\u4ecd\u672a\u8fbe\u5230\u672c\u6587\u8bbe\u7f6e\u7684\u6700\u4f4e\u8986\u76d6\u5341\u3002\u4e0d\u80fd\u56e0\u4e3a\u652f\u6301\u6bd4\u4f8b\u770b\u8d77\u6765\u662f\u767e\u5206\u4e4b\u767e\uff0c\u5c31\u628a\u8fd9\u4e2a\u4f4d\u70b9\u89c6\u4e3a\u901a\u8fc7\u5168\u90e8\u8d28\u91cf\u6761\u4ef6\u3002\u6bd4\u4f8b\u7684\u5206\u6bcd\u5f88\u5c0f\uff0c\u548c\u51e0\u5341\u6761\u72ec\u7acb\u89c2\u5bdf\u5f97\u5230\u540c\u4e00\u6bd4\u4f8b\u7684\u542b\u4e49\u4e0d\u540c\u3002<\/p>\n
\u771f\u5b9e\u5206\u6790\u9047\u5230\u4e00\u4e2a\u6837\u672c\u6bd4\u53e6\u4e00\u4e2a\u5c11\u51e0\u4e2a SNP\uff0c\u5e94\u5148\u68c0\u67e5\u8fd9\u4e9b\u4f4d\u7f6e\u7684\u6df1\u5ea6\u3001\u6bd4\u5bf9\u8d28\u91cf\u548c\u8fc7\u6ee4\u539f\u56e0\u3002\u628a\u672a\u62a5\u544a\u4f4d\u70b9\u7edf\u4e00\u8865\u6210\u53c2\u8003\uff0c\u4f1a\u628a\u4e0d\u53ef\u5224\u65ad\u72b6\u6001\u8f6c\u6362\u6210\u4e00\u4e2a\u786e\u5b9a\u7b54\u6848\u3002\u66f4\u5408\u7406\u7684\u7ed3\u679c\u8868\u5e94\u5141\u8bb8\u53ef\u9760\u53c2\u8003\u3001\u53ef\u9760\u66ff\u4ee3\u548c\u65e0\u6cd5\u5224\u65ad\u4e09\u7c7b\u72b6\u6001\u540c\u65f6\u5b58\u5728\u3002<\/p>\n
\u7b2c\u4e8c\u4e2a\u53d1\u73b0\uff0c\u5171\u8bc6\u6587\u4ef6\u5728\u7f3a\u8bc1\u636e\u7684\u4f4d\u7f6e\u4fdd\u7559\u4e86\u53c2\u8003\u78b1\u57fa<\/h2>\n
\u672c\u6b21\u68c0\u67e5\u7684\u5173\u952e\u4f4d\u7f6e\u662f\u7b2c\u4e00\u4e07\u4e94\u5343\u4f4d\uff0c\u53c2\u8003\u4e3a G\uff0c\u4e09\u4e2a\u6837\u672c\u7684\u8bbe\u8ba1\u771f\u503c\u90fd\u662f T\u3002\u6b63\u5e38\u8986\u76d6\u7ec4\u5728\u6bd4\u5bf9\u5e8f\u5217\u548c\u5171\u8bc6\u5e8f\u5217\u4e2d\u90fd\u4e3a T\u3002\u65e0\u8986\u76d6\u7ec4\u7684\u6bd4\u5bf9\u5e8f\u5217\u4e3a\u7f3a\u53e3\uff0c\u4f4e\u8986\u76d6\u7ec4\u7684\u6bd4\u5bf9\u5e8f\u5217\u4e3a N\uff0c\u4f46\u4e8c\u8005\u5171\u8bc6\u5e8f\u5217\u90fd\u4e3a\u53c2\u8003\u78b1\u57fa G\u3002<\/p>\n
\n\n\n\n\n\n\n\n
\u6587\u4ef6\u53ca\u4f4d\u7f6e<\/th>\n\u6b63\u5e38\u8986\u76d6<\/th>\n\u65e0\u8986\u76d6<\/th>\n\u4f4e\u8986\u76d6<\/th>\n<\/tr>\n<\/thead>\n
snps.tab \u662f\u5426\u6709 15000<\/td>\n\u6709<\/td>\n\u65e0<\/td>\n\u65e0<\/td>\n<\/tr>\n
snps.aligned.fa \u7684 15000<\/td>\nT<\/td>\n–<\/td>\nN<\/td>\n<\/tr>\n
snps.consensus.fa \u7684 15000<\/td>\nT<\/td>\nG<\/td>\nG<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u8fd9\u5f20\u5c0f\u8868\u5c55\u793a\u4e86\u4e3a\u4ec0\u4e48\u201c\u5171\u8bc6\u201d\u8fd9\u4e2a\u540d\u5b57\u4e0d\u80fd\u4ee3\u66ff\u6587\u4ef6\u7528\u9014\u8bf4\u660e\u3002\u5bf9\u672c\u6b21\u8f93\u51fa\u800c\u8a00\uff0c\u5171\u8bc6\u5e8f\u5217\u5e94\u7528\u4e86\u901a\u8fc7\u8fc7\u6ee4\u7684\u53d8\u5f02\uff0c\u4f46\u6ca1\u6709\u5728\u8fd9\u4e2a\u7f3a\u8bc1\u636e\u4f4d\u7f6e\u4fdd\u7559\u76f8\u540c\u7684\u7f3a\u5931\u6807\u8bb0\u3002\u82e5\u76f4\u63a5\u6bd4\u8f83\u4e09\u6761\u5171\u8bc6\u5e8f\u5217\uff0c\u5c31\u4f1a\u628a\u5df2\u77e5\u76f8\u540c\u7684\u6837\u672c\u771f\u503c\u8bef\u8bfb\u51fa\u5dee\u5f02\uff0c\u6216\u8005\u5728\u5176\u4ed6\u6bd4\u8f83\u91cc\u5236\u9020\u53c2\u8003\u4e00\u81f4\u7684\u5047\u8c61\u3002<\/p>\n
\u4e5f\u4e0d\u8981\u628a\u672c\u6b21\u6bd4\u5bf9\u5e8f\u5217\u89e3\u91ca\u4e3a\u4ec5\u5c06\u53c2\u8003\u6253\u4e0a\u8986\u76d6\u6807\u8bb0\u3002\u5b9e\u9645\u6587\u4ef6\u5df2\u7ecf\u5728\u901a\u8fc7\u6761\u4ef6\u7684\u4f4d\u7f6e\u5e26\u5165\u4e86\u66ff\u4ee3\u78b1\u57fa\u3002\u7b2c\u4e94\u5343\u548c\u7b2c\u4e8c\u4e07\u4e94\u5343\u4f4d\u5728\u4e09\u7ec4\u4e2d\u90fd\u662f A\uff0c\u6b63\u5e38\u8986\u76d6\u7ec4\u7684\u7b2c\u4e00\u4e07\u4e94\u5343\u4f4d\u662f T\u3002\u5e94\u4ee5\u6240\u7528\u7248\u672c\u7684\u771f\u5b9e\u8f93\u51fa\u53ca\u5bf9\u5e94\u5b9e\u73b0<\/a>\u6838\u5bf9\u6587\u4ef6\u8bed\u4e49\uff0c\u800c\u4e0d\u662f\u51ed\u6587\u4ef6\u540d\u6216\u65e7\u5370\u8c61\u505a\u9009\u62e9\u3002<\/p>\n
\u5982\u679c\u7814\u7a76\u95ee\u9898\u662f\u6837\u672c\u4e4b\u95f4\u7684\u53ef\u6bd4\u8f83\u5dee\u5f02\uff0c\u5e94\u9009\u62e9\u80fd\u4fdd\u7559\u4f4d\u7f6e\u5bf9\u5e94\u548c\u7f3a\u5931\u72b6\u6001\u7684\u7ed3\u679c\uff0c\u5e76\u660e\u786e\u7edf\u8ba1\u65f6\u6392\u9664\u54ea\u4e9b\u5b57\u7b26\u3002\u82e5\u7814\u7a76\u95ee\u9898\u9700\u8981\u5b8c\u6574\u7684\u66ff\u4ee3\u540e\u5e8f\u5217\uff0c\u5219\u8fd8\u5fc5\u987b\u8bf4\u660e\u54ea\u4e9b\u4f4d\u7f6e\u6ca1\u6709\u53ef\u9760\u89c2\u5bdf\u3002\u6ca1\u6709\u4e00\u79cd\u6587\u4ef6\u53ef\u4ee5\u4e0d\u52a0\u89e3\u91ca\u5730\u540c\u65f6\u6ee1\u8db3\u6240\u6709\u540e\u7eed\u76ee\u7684\u3002<\/p>\n
\u7b2c\u4e09\u4e2a\u53d1\u73b0\uff0c\u4e09\u4e07\u4e2a\u4f4d\u7f6e\u6700\u540e\u53ea\u5269\u4e24\u5217\u6838\u5fc3 SNP<\/h2>\n
\u5c06\u4e09\u7ec4\u7ed3\u679c\u4ea4\u7ed9\u6838\u5fc3\u6bd4\u5bf9\u7a0b\u5e8f\u540e\uff0c\u6bcf\u6761\u5168\u957f\u6bd4\u5bf9\u5e8f\u5217\u4ecd\u6709\u4e09\u4e07\u5217\uff0c\u800c\u6838\u5fc3 SNP \u6bd4\u5bf9\u6bcf\u6761\u53ea\u6709\u4e24\u5217\u3002\u8fd9\u4e24\u5217\u5bf9\u5e94\u4e09\u7ec4\u90fd\u53ef\u4ee5\u53ef\u9760\u6bd4\u8f83\u7684\u7b2c\u4e94\u5343\u4e0e\u7b2c\u4e8c\u4e07\u4e94\u5343\u4f4d\u3002\u6b63\u5e38\u8986\u76d6\u7ec4\u72ec\u6709\u8bc1\u636e\u652f\u6301\u7684\u7b2c\u4e00\u4e07\u4e94\u5343\u4f4d\uff0c\u6ca1\u6709\u8fdb\u5165\u5171\u540c\u6838\u5fc3 SNP \u96c6\u5408\u3002<\/p>\n
snippy-core --ref reference.fna --prefix core covered gap low\r\nsnippy-clean_full_aln core.full.aln > clean.full.aln\r\n<\/code><\/pre>\n
\u8fd9\u4e00\u73b0\u8c61\u89e3\u91ca\u4e86\u4e00\u4e2a\u5e38\u89c1\u9879\u76ee\u95ee\u9898\u3002\u589e\u52a0\u4f4e\u8d28\u91cf\u6837\u672c\u540e\uff0c\u6838\u5fc3 SNP \u6570\u91cf\u53ef\u80fd\u51cf\u5c11\uff0c\u5e76\u4e0d\u8868\u793a\u524d\u9762\u6837\u672c\u7684\u771f\u5b9e\u5dee\u5f02\u7a81\u7136\u6d88\u5931\uff0c\u800c\u662f\u5171\u540c\u53ef\u6bd4\u8f83\u96c6\u5408\u53d1\u751f\u4e86\u6539\u53d8\u3002\u6837\u672c\u7b5b\u9009\u4e0e\u6838\u5fc3\u5b9a\u4e49\u5171\u540c\u51b3\u5b9a\u4e86\u5206\u6790\u5206\u6bcd\uff0c\u4e0d\u80fd\u628a\u4e0d\u540c\u6837\u672c\u96c6\u5408\u751f\u6210\u7684\u77e9\u9635\u5f53\u6210\u540c\u4e00\u5c3a\u5ea6\u7684\u76f4\u63a5\u6bd4\u8f83\u3002<\/p>\n
\u56e0\u6b64\u62a5\u544a SNP \u8ddd\u79bb\u65f6\uff0c\u6700\u597d\u540c\u65f6\u8bf4\u660e\u53ef\u6bd4\u8f83\u4f4d\u70b9\u6570\u91cf\u6216\u4f7f\u7528\u7684\u5171\u540c\u6838\u5fc3\u8303\u56f4\u3002\u4e24\u4e2a\u6837\u672c\u5728\u5f88\u5c11\u7684\u53ef\u6bd4\u8f83\u4f4d\u7f6e\u4e0a\u6ca1\u6709\u5dee\u5f02\uff0c\u548c\u5728\u5927\u90e8\u5206\u57fa\u56e0\u7ec4\u4e0a\u90fd\u6ca1\u6709\u5dee\u5f02\uff0c\u8bc1\u636e\u5f3a\u5ea6\u663e\u7136\u4e0d\u540c\u3002\u5355\u72ec\u4e00\u4e2a\u96f6\u5dee\u5f02\u6570\u5b57\uff0c\u4f1a\u9690\u85cf\u8fd9\u79cd\u5dee\u522b\u3002<\/p>\n
\u672c\u6b21\u4e09\u7ec4\u5176\u5b9e\u62e5\u6709\u5b8c\u5168\u76f8\u540c\u7684\u8bbe\u8ba1\u57fa\u56e0\u578b\uff0c\u53ea\u662f\u6d4b\u5e8f\u89c2\u5bdf\u4e0d\u540c\u3002\u6838\u5fc3 SNP \u6bd4\u5bf9\u4e2d\u8fd8\u5305\u542b\u53c2\u8003\u5e8f\u5217\uff0c\u6240\u4ee5\u4fdd\u7559\u4e86\u6837\u672c\u5171\u540c\u76f8\u5bf9\u53c2\u8003\u7684\u4e24\u4e2a\u66ff\u6362\u3002\u4e0d\u8981\u770b\u5230\u77e9\u9635\u5b58\u5728\u4e24\u5217\uff0c\u5c31\u8bef\u5199\u6210\u4e09\u4e2a\u8bbe\u8ba1\u6837\u672c\u5f7c\u6b64\u6709\u4e24\u4e2a\u5dee\u5f02\u3002\u89e3\u91ca\u8ddd\u79bb\u65f6\u8fd8\u9700\u8981\u770b\u6e05\u6bd4\u8f83\u5bf9\u8c61\u662f\u5426\u5305\u542b\u53c2\u8003\u3002<\/p>\n
\u6e05\u7406\u5168\u957f\u6bd4\u5bf9\u65f6\u4fdd\u7559\u5750\u6807<\/h2>\n
\u6838\u5fc3\u5168\u957f\u6bd4\u5bf9\u4e2d\u7684\u66ff\u4ee3\u78b1\u57fa\u4ee5\u5c0f\u5199\u51fa\u73b0\uff0c\u672c\u6b21\u6b63\u5e38\u8986\u76d6\u7ec4\u76ee\u6807\u4f4d\u7f6e\u4e3a\u5c0f\u5199 t\u3002\u6e05\u7406\u7a0b\u5e8f\u5148\u8f6c\u6210\u5927\u5199\uff0c\u518d\u66ff\u6362\u4e0d\u5141\u8bb8\u7684\u5b57\u7b26\uff0c\u56e0\u6b64\u8be5\u4f4d\u7f6e\u53d8\u4e3a T\u3002\u539f\u6709 N \u548c\u7f3a\u53e3\u7b26\u53f7\u4fdd\u6301\u5176\u76f8\u5e94\u5f62\u5f0f\uff0c\u6e05\u7406\u540e\u7684\u6bcf\u6761\u5e8f\u5217\u4ecd\u4e3a\u4e09\u4e07\u5217\u3002<\/p>\n
\u8fd9\u91cc\u7684\u6e05\u7406\u4e0d\u662f\u628a\u6240\u6709\u7f3a\u5931\u4f4d\u7f6e\u5220\u9664\uff0c\u4e5f\u4e0d\u662f\u5c06\u6240\u6709\u7f3a\u53e3\u90fd\u53d8\u4e3a N\u3002\u8be5\u7248\u672c\u6e05\u7406\u811a\u672c<\/a>\u4fdd\u7559 A\u3001C\u3001G\u3001T\u3001N \u548c\u7f3a\u53e3\u5b57\u7b26\u3002\u8fd0\u884c\u540e\u540c\u65f6\u68c0\u67e5\u957f\u5ea6\u548c\u5b57\u7b26\u96c6\u5408\uff0c\u662f\u4e00\u79cd\u6210\u672c\u5f88\u4f4e\u4f46\u5f88\u6709\u6548\u7684\u6838\u67e5\u65b9\u5f0f\u3002<\/p>\n
\u82e5\u4e0b\u6e38\u65b9\u6cd5\u9700\u8981\u53d8\u5f02\u5728\u57fa\u56e0\u7ec4\u4e2d\u7684\u7a7a\u95f4\u5206\u5e03\uff0c\u4f8b\u5982\u968f\u540e\u5206\u6790\u5c40\u90e8\u53d8\u5f02\u805a\u96c6\uff0c\u5c31\u5e94\u4fdd\u7559\u8fd9\u79cd\u5168\u957f\u5750\u6807\u3002\u53ea\u6709\u4e24\u5217\u7684\u6838\u5fc3 SNP \u77e9\u9635\u5df2\u7ecf\u4e22\u5931\u539f\u6765\u7684\u95f4\u9694\uff0c\u4e0d\u80fd\u7528\u6539\u6587\u4ef6\u540d\u7684\u65b9\u6cd5\u6062\u590d\u3002\u6e05\u7406\u5b57\u7b26\u548c\u5220\u9664\u4e0d\u53d8\u4f4d\u70b9\u662f\u4e24\u79cd\u5b8c\u5168\u4e0d\u540c\u7684\u64cd\u4f5c\uff0c\u9700\u8981\u5206\u522b\u8bb0\u5f55\u3002<\/p>\n
\u4ece\u8fd9\u6b21\u5bf9\u7167\u5f62\u6210\u5b9e\u9645\u9879\u76ee\u7684\u68c0\u67e5\u987a\u5e8f<\/h2>\n
\u5148\u67e5\u770b\u6bcf\u4e2a\u6837\u672c\u80fd\u53ef\u9760\u8986\u76d6\u591a\u5c11\u53c2\u8003\u4f4d\u7f6e\uff0c\u518d\u770b\u4f4e\u8986\u76d6\u3001\u65e0\u8986\u76d6\u53ca\u5f02\u5e38\u72b6\u6001\u5206\u5e03\u3002\u82e5\u67d0\u4e2a\u6837\u672c\u660e\u663e\u504f\u79bb\u5176\u4ed6\u6837\u672c\uff0c\u5e94\u68c0\u67e5\u539f\u59cb\u6570\u636e\u8d28\u91cf\u3001\u53c2\u8003\u9002\u914d\u6027\u548c\u6bd4\u5bf9\u60c5\u51b5\u3002\u6b64\u65f6\u76f4\u63a5\u6269\u5927\u6837\u672c\u96c6\u5408\u751f\u6210\u6838\u5fc3\u77e9\u9635\uff0c\u53ef\u80fd\u8ba9\u6240\u6709\u6837\u672c\u5171\u540c\u53ef\u7528\u7684\u8303\u56f4\u90fd\u88ab\u62c9\u4f4e\u3002<\/p>\n
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