{"id":72724,"date":"2026-11-15T10:12:51","date_gmt":"2026-11-15T02:12:51","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=72724"},"modified":"2026-11-15T10:14:25","modified_gmt":"2026-11-15T02:14:25","slug":"coverm-relative-abundance-unmapped-breadth-denominator","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/coverm-relative-abundance-unmapped-breadth-denominator\/","title":{"rendered":"CoverM \u7684\u76f8\u5bf9\u4e30\u5ea6\u4e3a\u4ec0\u4e48\u53d8\u4e86\uff1f\u7528 100 \u6761\u8bfb\u6bb5\u5b9e\u8dd1\u8986\u76d6\u6df1\u5ea6\u3001\u8986\u76d6\u5e7f\u5ea6\u548c\u672a\u6bd4\u5bf9\u5206\u6bcd"},"content":{"rendered":"
\n

\u540c\u4e00\u4efd\u5b8f\u57fa\u56e0\u7ec4\u6570\u636e\uff0c\u8fc7\u6ee4\u524d\u540e\u5e73\u5747\u8986\u76d6\u6df1\u5ea6\u76f8\u540c\uff0c\u76f8\u5bf9\u4e30\u5ea6\u5374\u53ef\u80fd\u660e\u663e\u53d8\u5316\u3002\u9047\u5230\u8fd9\u79cd\u60c5\u51b5\uff0c\u5148\u68c0\u67e5\u53c2\u4e0e\u8ba1\u7b97\u7684\u8bfb\u6bb5\u96c6\u5408\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u957f\u5ea6\u548c\u8fc7\u6ee4\u6761\u4ef6\uff0c\u5f80\u5f80\u80fd\u591f\u89e3\u91ca\u5dee\u5f02\u3002\u5c24\u5176\u662f\u63d0\u524d\u5220\u9664\u672a\u6bd4\u5bf9\u8bb0\u5f55\uff0c\u6216\u8005\u628a\u8986\u76d6\u5e7f\u5ea6\u95e8\u69db\u8bbe\u5f97\u66f4\u4e25\u683c\uff0c\u90fd\u53ef\u80fd\u6539\u53d8\u6700\u7ec8\u4e30\u5ea6\u8868\u7684\u542b\u4e49\u3002<\/p>\n

\u672c\u6587\u5b89\u88c5 CoverM 0.8.0\uff0c\u6784\u9020\u4e00\u4efd\u53ef\u4ee5\u624b\u5de5\u6838\u7b97\u7684\u767e\u6761\u8bfb\u6bb5\u6bd4\u5bf9\u6587\u4ef6\uff0c\u5b9e\u9645\u8fd0\u884c\u4e09\u7ec4\u8986\u76d6\u7edf\u8ba1\uff0c\u5e76\u53e6\u5916\u68c0\u67e5\u8bfb\u6bb5\u8ba1\u6570\u4e0e\u5e7f\u5ea6\u8fc7\u6ee4\u7684\u7ec4\u5408\u3002\u5b9e\u9a8c\u76f4\u63a5\u4f7f\u7528\u8bbe\u8ba1\u597d\u7684\u6bd4\u5bf9\u8bb0\u5f55\uff0c\u501f\u52a9 samtools \u8f6c\u6210\u6392\u5e8f\u540e\u7684 BAM\uff0c\u91cd\u70b9\u9a8c\u8bc1 CoverM \u5728\u8fd9\u4e9b\u8f93\u5165\u6761\u4ef6\u4e0b\u600e\u6837\u8ba1\u7b97\u548c\u62a5\u544a\u7ed3\u679c\u3002<\/p>\n

\"\u6df1\u5ea6\u76f8\u540c\uff0c\u4e30\u5ea6\u4e3a\u4f55\u53d8\u4e86\u3002\u7528
\u7528 100 \u6761\u53d7\u63a7\u6bd4\u5bf9\u8bb0\u5f55\u6838\u5bf9\u5206\u6bcd<\/figcaption><\/figure>\n

\u5148\u5206\u6e05\u6df1\u5ea6\u3001\u5e7f\u5ea6\u548c\u76f8\u5bf9\u4e30\u5ea6<\/h2>\n

\u5e73\u5747\u8986\u76d6\u6df1\u5ea6\u63cf\u8ff0\u53c2\u8003\u5e8f\u5217\u6bcf\u4e2a\u4f4d\u7f6e\u5e73\u5747\u88ab\u591a\u5c11\u6761\u8bfb\u6bb5\u8986\u76d6\u3002\u8986\u76d6\u5e7f\u5ea6\u63cf\u8ff0\u53c2\u8003\u5e8f\u5217\u4e2d\u6709\u591a\u5c11\u6bd4\u4f8b\u7684\u4f4d\u7f6e\u81f3\u5c11\u5f97\u5230\u4e00\u6b21\u8986\u76d6\u3002\u4e24\u8005\u53ef\u4ee5\u540c\u65f6\u5f88\u9ad8\uff0c\u4e5f\u53ef\u80fd\u4e00\u4e2a\u9ad8\u3001\u53e6\u4e00\u4e2a\u4f4e\u3002<\/p>\n

\u4f8b\u5982\uff0c\u4e00\u5343\u6761\u8bfb\u6bb5\u96c6\u4e2d\u8986\u76d6\u540c\u4e00\u4e2a\u77ed\u533a\u57df\uff0c\u4f1a\u8ba9\u8fd9\u4e2a\u533a\u57df\u5806\u79ef\u51fa\u5f88\u9ad8\u7684\u6df1\u5ea6\uff0c\u4f46\u57fa\u56e0\u7ec4\u5176\u4ed6\u4f4d\u7f6e\u4ecd\u7136\u6ca1\u6709\u8bc1\u636e\u3002\u82e5\u5c06\u6240\u6709\u4f4d\u7f6e\u4e00\u8d77\u5e73\u5747\uff0c\u5f97\u5230\u7684\u5e73\u5747\u6df1\u5ea6\u53ef\u4ee5\u5927\u4e8e\u4e00\uff0c\u8986\u76d6\u5e7f\u5ea6\u5374\u4ecd\u7136\u5f88\u4f4e\u3002\u56e0\u6b64\uff0c\u5224\u65ad\u67d0\u4e2a\u57fa\u56e0\u7ec4\u5728\u6837\u672c\u4e2d\u662f\u5426\u5f97\u5230\u5145\u5206\u652f\u6301\u65f6\uff0c\u4e24\u4e2a\u6307\u6807\u503c\u5f97\u4e00\u8d77\u68c0\u67e5\u3002<\/p>\n

CoverM \u53ef\u4ee5\u6309\u7247\u6bb5\u6216\u57fa\u56e0\u7ec4\u6c47\u603b\u591a\u79cd\u8986\u76d6\u6307\u6807\u3002\u57fa\u56e0\u7ec4\u6a21\u5f0f\u7684\u76f8\u5bf9\u4e30\u5ea6\u8fd8\u4f1a\u8003\u8651\u4e0d\u540c\u53c2\u8003\u957f\u5ea6\u548c\u5b9e\u9645\u5f97\u5230\u652f\u6301\u7684\u8bfb\u6bb5\u6bd4\u4f8b\u3002\u4f7f\u7528\u8fd9\u4e9b\u6307\u6807\u65f6\uff0c\u9700\u8981\u540c\u65f6\u8bb0\u5f55\u8ba1\u7b97\u65b9\u6cd5\u548c\u8fc7\u6ee4\u53c2\u6570\u3002CoverM \u5b98\u65b9\u9879\u76ee\u8bf4\u660e<\/a><\/p>\n

\u672c\u6b21\u6240\u6709\u6761\u4ef6\u90fd\u628a\u7247\u6bb5\u4e24\u7aef\u6392\u9664\u957f\u5ea6\u8bbe\u4e3a\u96f6\u3002\u8fd9\u6837\uff0c\u53c2\u8003\u7684\u5168\u90e8\u4f4d\u7f6e\u90fd\u53c2\u4e0e\u5e73\u5747\u6df1\u5ea6\u8ba1\u7b97\uff0c\u65b9\u4fbf\u624b\u5de5\u590d\u7b97\u3002\u6b63\u5f0f\u9879\u76ee\u662f\u5426\u6392\u9664\u7247\u6bb5\u4e24\u7aef\uff0c\u5e94\u7ed3\u5408\u6bd4\u5bf9\u65b9\u5f0f\u3001\u7247\u6bb5\u957f\u5ea6\u5206\u5e03\u548c\u672b\u7aef\u8986\u76d6\u60c5\u51b5\u51b3\u5b9a\uff0c\u5e76\u4fdd\u6301\u4e0d\u540c\u6837\u672c\u4e4b\u95f4\u7684\u7edf\u8ba1\u53e3\u5f84\u4e00\u81f4\u3002<\/p>\n

\u4e00\u767e\u6761\u8bfb\u6bb5\u5982\u4f55\u6784\u6210\u8fd9\u4e2a\u5b9e\u9a8c<\/h2>\n

\u53c2\u8003\u96c6\u5408\u5305\u542b\u4e24\u4e2a\u6559\u5b66\u57fa\u56e0\u7ec4\u3002\u7532\u7684\u957f\u5ea6\u4e3a\u4e00\u5343\u78b1\u57fa\uff0c\u4e59\u7684\u957f\u5ea6\u4e3a\u4e24\u5343\u78b1\u57fa\u3002\u6bcf\u6761\u8bfb\u6bb5\u957f\u5ea6\u90fd\u662f\u4e00\u767e\u78b1\u57fa\uff0c\u6240\u6709\u5df2\u6bd4\u5bf9\u8bfb\u6bb5\u5747\u4e3a\u65e0\u9519\u914d\u7684\u5b8c\u6574\u5339\u914d\u3002<\/p>\n

\u7532\u83b7\u5f97\u5341\u6761\u8bfb\u6bb5\uff0c\u5206\u522b\u8986\u76d6\u8fde\u7eed\u7684\u5341\u4e2a\u4e00\u767e\u78b1\u57fa\u533a\u95f4\uff0c\u56e0\u6b64\u6bcf\u4e2a\u4f4d\u7f6e\u6070\u597d\u8986\u76d6\u4e00\u6b21\u3002\u4e59\u83b7\u5f97\u4e94\u5341\u6761\u8bfb\u6bb5\uff0c\u5168\u90e8\u5806\u5728\u540c\u4e00\u4e2a\u4e00\u767e\u78b1\u57fa\u533a\u95f4\u3002\u5176\u4f59\u56db\u5341\u6761\u8bfb\u6bb5\u4ee5\u672a\u6bd4\u5bf9\u8bb0\u5f55\u7684\u5f62\u5f0f\u4fdd\u5b58\u5728\u6587\u4ef6\u4e2d\u3002\u8fd9\u91cc\u4f7f\u7528\u53ef\u63a7\u8f93\u5165\uff0c\u662f\u4e3a\u4e86\u628a\u7edf\u8ba1\u89c4\u5219\u4e0e\u6bd4\u5bf9\u7b97\u6cd5\u7684\u5dee\u5f02\u5206\u5f00\u89c2\u5bdf\u3002<\/p>\n

\u7531\u8f93\u5165\u8bbe\u8ba1\u53ef\u76f4\u63a5\u7b97\u51fa\uff0c\u7532\u7684\u5e73\u5747\u6df1\u5ea6\u4e3a\u4e00\uff0c\u8986\u76d6\u5e7f\u5ea6\u4e3a\u767e\u5206\u4e4b\u767e\u3002\u4e59\u7684\u7d2f\u8ba1\u8986\u76d6\u78b1\u57fa\u6570\u4e3a\u4e94\u5343\uff0c\u9664\u4ee5\u4e24\u5343\u78b1\u57fa\u5f97\u5230\u5e73\u5747\u6df1\u5ea6\u4e8c\u70b9\u4e94\uff0c\u4f46\u5b9e\u9645\u8986\u76d6\u4f4d\u7f6e\u53ea\u6709\u4e00\u767e\uff0c\u8986\u76d6\u5e7f\u5ea6\u4e3a\u767e\u5206\u4e4b\u4e94\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u57fa\u56e0\u7ec4<\/th>\n\u957f\u5ea6<\/th>\n\u5df2\u6bd4\u5bf9\u8bfb\u6bb5\u6570<\/th>\n\u5e73\u5747\u6df1\u5ea6<\/th>\n\u8986\u76d6\u5e7f\u5ea6<\/th>\n<\/tr>\n<\/thead>\n
\u7532<\/td>\n1,000 bp<\/td>\n10<\/td>\n1<\/td>\n100%<\/td>\n<\/tr>\n
\u4e59<\/td>\n2,000 bp<\/td>\n50<\/td>\n2.5<\/td>\n5%<\/td>\n<\/tr>\n
\u672a\u6bd4\u5bf9\u8bb0\u5f55<\/td>\n\u4e0d\u9002\u7528<\/td>\n40<\/td>\n\u4e0d\u9002\u7528<\/td>\n\u4e0d\u9002\u7528<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u9644\u5e26\u811a\u672c\u81ea\u52a8\u521b\u5efa\u53c2\u8003\u5e8f\u5217\u3001\u6bd4\u5bf9\u8bb0\u5f55\u548c\u57fa\u56e0\u7ec4\u5b9a\u4e49\u8868\uff0c\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\u540e\u53ef\u4ee5\u91cd\u590d\u751f\u6210\u76f8\u540c\u8f93\u5165\u3002\u6bd4\u5bf9\u8bb0\u5f55\u4e2d\u7684\u53c2\u8003\u540d\u79f0\u4e0e\u5b9a\u4e49\u8868\u5b8c\u5168\u4e00\u81f4\uff0c\u6240\u6709\u8bfb\u6bb5\u6807\u8bc6\u552f\u4e00\uff0c\u5e76\u4e14\u6ca1\u6709\u6b21\u7ea7\u6216\u8865\u5145\u6bd4\u5bf9\u8bb0\u5f55\uff0c\u4fbf\u4e8e\u96c6\u4e2d\u89c2\u5bdf\u672c\u6b21\u5173\u6ce8\u7684\u4e24\u4e2a\u53c2\u6570\u53d8\u5316\u3002<\/p>\n

\u7b2c\u4e00\u7ec4\u4fdd\u7559\u5168\u90e8\u8bb0\u5f55\uff0c\u5173\u95ed\u8986\u76d6\u5e7f\u5ea6\u8fc7\u6ee4<\/h2>\n

\u57fa\u56e0\u7ec4\u5b9a\u4e49\u8868\u4f7f\u7528\u4e24\u5217\uff0c\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u7ec4\u540d\u79f0\uff0c\u7b2c\u4e8c\u5217\u4e3a\u5c5e\u4e8e\u8be5\u57fa\u56e0\u7ec4\u7684\u53c2\u8003\u7247\u6bb5\u540d\u79f0\u3002\u5b9e\u9645\u9879\u76ee\u4e2d\uff0c\u4e00\u4e2a\u57fa\u56e0\u7ec4\u53ef\u4ee5\u5bf9\u5e94\u591a\u6761\u7247\u6bb5\uff0c\u9700\u8981\u628a\u5168\u90e8\u5bf9\u5e94\u5173\u7cfb\u5217\u51fa\u6765\u3002\u6574\u7406\u5b9a\u4e49\u8868\u65f6\uff0c\u5e94\u68c0\u67e5\u7247\u6bb5\u662f\u5426\u9057\u6f0f\uff0c\u4ee5\u53ca\u540c\u4e00\u4e2a\u7247\u6bb5\u662f\u5426\u610f\u5916\u91cd\u590d\u5f52\u5165\u591a\u4e2a\u57fa\u56e0\u7ec4\u3002<\/p>\n

printf 'Genome_A\\ta\\nGenome_B\\tb\\n' > genomes.tsv\r\n<\/code><\/pre>\n
\u672c\u6b21\u8fd0\u884c\u7684\u6838\u5fc3\u547d\u4ee4\u5982\u4e0b\u3002\u8f93\u5165\u5df2\u7ecf\u6392\u5e8f\uff0c\u547d\u4ee4\u76f4\u63a5\u8bfb\u53d6 BAM \u5e76\u7edf\u8ba1\u5e73\u5747\u6df1\u5ea6\u3001\u8986\u76d6\u5e7f\u5ea6\u548c\u76f8\u5bf9\u4e30\u5ea6\u3002\u53c2\u6570\u503c\u53ca\u7a0b\u5e8f\u7248\u672c\u53ef\u4ee5\u5728\u9644\u5e26\u65e5\u5fd7\u548c\u7ed3\u679c\u8bb0\u5f55\u4e2d\u6838\u5bf9\u3002\u672c\u6b21 CoverM \u53d1\u5e03\u7248\u672c<\/a><\/p>\n
coverm genome \\\r\n  --bam-files all_reads.bam \\\r\n  --genome-definition genomes.tsv \\\r\n  --methods mean covered_fraction relative_abundance \\\r\n  --min-covered-fraction 0 \\\r\n  --contig-end-exclusion 0 \\\r\n  --threads 2 \\\r\n  --output-file all_no_breadth_filter.tsv\r\n<\/code><\/pre>\n
\u5b9e\u9645\u8f93\u51fa\u4e2d\uff0c\u7532\u7684\u5e73\u5747\u6df1\u5ea6\u4e3a\u4e00\uff0c\u4e59\u4e3a\u4e8c\u70b9\u4e94\uff0c\u5e7f\u5ea6\u5206\u522b\u4e3a\u4e00\u548c\u96f6\u70b9\u96f6\u4e94\uff0c\u4e0e\u624b\u7b97\u4e00\u81f4\u3002\u7532\u7684\u76f8\u5bf9\u4e30\u5ea6\u7ea6\u4e3a\u767e\u5206\u4e4b\u5341\u4e03\u70b9\u4e00\u56db\uff0c\u4e59\u7ea6\u4e3a\u767e\u5206\u4e4b\u56db\u5341\u4e8c\u70b9\u516b\u516d\uff0c\u672a\u6bd4\u5bf9\u884c\u7ea6\u4e3a\u767e\u5206\u4e4b\u56db\u5341\u3002<\/p>\n
\u7406\u89e3\u8fd9\u7ec4\u4e30\u5ea6\u65f6\uff0c\u53ef\u4ee5\u5148\u6309\u5e73\u5747\u6df1\u5ea6\u5206\u914d\u4e24\u8005\u7684\u76f8\u5bf9\u4efd\u989d\u3002\u7532\u5360\u4e00\u9664\u4ee5\u4e09\u70b9\u4e94\uff0c\u4e59\u5360\u4e8c\u70b9\u4e94\u9664\u4ee5\u4e09\u70b9\u4e94\uff0c\u518d\u4e58\u4ee5\u516d\u5341\u6761\u5df2\u6bd4\u5bf9\u8bfb\u6bb5\u5360\u5168\u90e8\u4e00\u767e\u6761\u7684\u6bd4\u4f8b\u3002\u8fd9\u5c31\u5f97\u5230\u5de5\u5177\u672c\u6b21\u62a5\u544a\u7684\u4e24\u4e2a\u767e\u5206\u6bd4\u3002<\/p>\n
mapped_fraction = 60 \/ 100\r\na_percent = 1 \/ (1 + 2.5) * mapped_fraction * 100\r\nb_percent = 2.5 \/ (1 + 2.5) * mapped_fraction * 100\r\nprint(a_percent, b_percent)\r\n<\/code><\/pre>\n
\u7532\u53ea\u6709\u5341\u6761\u5df2\u6bd4\u5bf9\u8bfb\u6bb5\uff0c\u5374\u5f97\u5230\u7ea6\u767e\u5206\u4e4b\u5341\u4e03\u70b9\u4e00\u56db\u7684\u4e30\u5ea6\uff0c\u539f\u56e0\u5c31\u5728\u4e8e\u53c2\u8003\u957f\u5ea6\u53c2\u4e0e\u4e86\u8986\u76d6\u8ba1\u7b97\u3002\u5c06\u57fa\u56e0\u7ec4\u76f8\u5bf9\u4e30\u5ea6\u4e0e\u539f\u59cb\u8bfb\u6bb5\u5360\u6bd4\u76f4\u63a5\u7b49\u540c\uff0c\u4f1a\u5ffd\u7565\u8fd9\u4e00\u6b65\u5f52\u4e00\u5316\u3002<\/p>\n
\u7b2c\u4e8c\u7ec4\u52a0\u5165\u767e\u5206\u4e4b\u5341\u7684\u8986\u76d6\u5e7f\u5ea6\u95e8\u69db<\/h2>\n
\u7b2c\u4e8c\u6b21\u8fd0\u884c\u4fdd\u6301\u540c\u4e00\u4efd BAM\uff0c\u552f\u4e00\u6539\u52a8\u662f\u5c06\u6700\u5c0f\u8986\u76d6\u5e7f\u5ea6\u8bbe\u4e3a\u767e\u5206\u4e4b\u5341\u3002\u5728\u672c\u6b21\u7248\u672c\u7684\u547d\u4ee4\u4e2d\u4f7f\u7528 --min-covered-fraction 10<\/code>\uff0c\u65e5\u5fd7\u786e\u8ba4\u91c7\u7528\u767e\u5206\u4e4b\u5341\u95e8\u69db\u3002<\/p>\n
\u4e59\u53ea\u6709\u767e\u5206\u4e4b\u4e94\u7684\u53c2\u8003\u4f4d\u7f6e\u83b7\u5f97\u8986\u76d6\uff0c\u56e0\u6b64\u88ab\u7f6e\u4e3a\u96f6\u3002\u8f93\u51fa\u4e2d\u7684\u5e73\u5747\u6df1\u5ea6\u3001\u8986\u76d6\u5e7f\u5ea6\u548c\u76f8\u5bf9\u4e30\u5ea6\u90fd\u53d8\u6210\u96f6\u3002\u7532\u4ecd\u7136\u4fdd\u7559\uff0c\u5e73\u5747\u6df1\u5ea6\u4e3a\u4e00\u3001\u5e7f\u5ea6\u4e3a\u4e00\uff0c\u4f46\u76f8\u5bf9\u4e30\u5ea6\u53d8\u6210\u767e\u5206\u4e4b\u5341\uff0c\u672a\u6bd4\u5bf9\u884c\u53d8\u6210\u767e\u5206\u4e4b\u4e5d\u5341\u3002<\/p>\n
\n\n\n\n\n\n\n\n
\u6761\u4ef6<\/th>\n\u7532\u76f8\u5bf9\u4e30\u5ea6<\/th>\n\u4e59\u76f8\u5bf9\u4e30\u5ea6<\/th>\n\u8f93\u51fa\u7684 unmapped<\/th>\n<\/tr>\n<\/thead>\n
\u4fdd\u7559\u5168\u90e8\u8bb0\u5f55\uff0c\u5e7f\u5ea6\u95e8\u69db\u4e3a\u96f6<\/td>\n17.1429%<\/td>\n42.8571%<\/td>\n40%<\/td>\n<\/tr>\n
\u4fdd\u7559\u5168\u90e8\u8bb0\u5f55\uff0c\u5e7f\u5ea6\u95e8\u69db\u4e3a 10%<\/td>\n10%<\/td>\n0%<\/td>\n90%<\/td>\n<\/tr>\n
\u4ec5\u4fdd\u7559\u5df2\u6bd4\u5bf9\u8bb0\u5f55\uff0c\u5e7f\u5ea6\u95e8\u69db\u4e3a\u96f6<\/td>\n28.5714%<\/td>\n71.4286%<\/td>\n0%<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u7b2c\u4e8c\u7ec4\u7684\u672a\u6bd4\u5bf9\u884c\u5c24\u5176\u503c\u5f97\u8ba4\u771f\u89e3\u91ca\u3002\u8f93\u5165\u6587\u4ef6\u4ecd\u6709\u516d\u5341\u6761\u5e26\u6709\u6bd4\u5bf9\u4f4d\u7f6e\u7684\u8bb0\u5f55\uff0c\u8bfb\u6bb5\u6807\u5fd7\u4e5f\u4fdd\u6301\u539f\u6837\u3002\u8868\u683c\u91cc\u62a5\u544a\u7684\u767e\u5206\u4e4b\u4e5d\u5341\uff0c\u662f\u7ed3\u5408\u57fa\u56e0\u7ec4\u5c42\u9762\u7684\u8fc7\u6ee4\u6761\u4ef6\u540e\u5f97\u5230\u7684\u7edf\u8ba1\u7ed3\u679c\uff0c\u5305\u542b\u4e86\u6ca1\u6709\u901a\u8fc7\u8fd9\u4e00\u95e8\u69db\u7684\u53c2\u8003\u6240\u5bf9\u5e94\u7684\u8bfb\u6bb5\u5f71\u54cd\u3002<\/p>\n
\u56e0\u6b64\uff0c\u5982\u679c\u60f3\u77e5\u9053\u539f\u59cb\u6bd4\u5bf9\u7a0b\u5e8f\u7a76\u7adf\u6709\u591a\u5c11\u8bfb\u6bb5\u83b7\u5f97\u4f4d\u7f6e\uff0c\u5e94\u67e5\u770b\u8f93\u5165\u6bd4\u5bf9\u6587\u4ef6\u7684\u6807\u5fd7\u7edf\u8ba1\u3002\u5982\u679c\u60f3\u77e5\u9053\u5728\u5f53\u524d\u8fc7\u6ee4\u6761\u4ef6\u4e0b\uff0c\u8fd8\u6709\u591a\u5c11\u8bfb\u6bb5\u672a\u8ba1\u5165\u5408\u683c\u53c2\u8003\uff0c\u5219\u8981\u7ed3\u5408 CoverM \u7684\u8f93\u51fa\u53e3\u5f84\u3002\u62a5\u544a\u8fd9\u4e24\u4e2a\u6570\u5b57\u65f6\uff0c\u628a\u5b83\u4eec\u5404\u81ea\u5bf9\u5e94\u7684\u6b65\u9aa4\u5199\u6e05\u695a\uff0c\u8bfb\u8005\u624d\u5bb9\u6613\u7406\u89e3\u5dee\u5f02\u3002<\/p>\n
\u8fd9\u7ec4\u5bf9\u7167\u4e5f\u5c55\u793a\u4e86\u5e7f\u5ea6\u95e8\u69db\u7684\u7528\u9014\u3002\u4e94\u5341\u6761\u8bfb\u6bb5\u96c6\u4e2d\u5728\u4e00\u4e2a\u77ed\u533a\u57df\uff0c\u7ed9\u51fa\u4e86\u76f8\u5f53\u9ad8\u7684\u5e73\u5747\u6df1\u5ea6\uff0c\u4f46\u652f\u6301\u8303\u56f4\u6709\u9650\u3002\u95e8\u69db\u80fd\u591f\u5e2e\u52a9\u8bc6\u522b\u8fd9\u79cd\u5c40\u90e8\u4fe1\u53f7\uff0c\u81f3\u4e8e\u5b83\u6765\u81ea\u4fdd\u5b88\u533a\u57df\u3001\u91cd\u590d\u5e8f\u5217\u8fd8\u662f\u5176\u4ed6\u539f\u56e0\uff0c\u8fd8\u9700\u8981\u68c0\u67e5\u771f\u5b9e\u6bd4\u5bf9\u4f4d\u7f6e\u548c\u53c2\u8003\u5185\u5bb9\u3002<\/p>\n
\u7b2c\u4e09\u7ec4\u63d0\u524d\u5220\u6389\u672a\u6bd4\u5bf9\u8bb0\u5f55<\/h2>\n
\u7b2c\u4e09\u7ec4\u5148\u7528 samtools \u5220\u9664\u56db\u5341\u6761\u672a\u6bd4\u5bf9\u8bb0\u5f55\uff0c\u5f97\u5230\u53ea\u542b\u516d\u5341\u6761\u5df2\u6bd4\u5bf9\u8bb0\u5f55\u7684\u6587\u4ef6\uff0c\u518d\u4f7f\u7528\u7b2c\u4e00\u7ec4\u7684\u7edf\u8ba1\u53c2\u6570\u3002\u7532\u548c\u4e59\u7684\u5e73\u5747\u6df1\u5ea6\u53ca\u8986\u76d6\u5e7f\u5ea6\u5168\u90e8\u76f8\u540c\uff0c\u4e30\u5ea6\u5374\u5206\u522b\u5347\u5230\u7ea6\u767e\u5206\u4e4b\u4e8c\u5341\u516b\u70b9\u4e94\u4e03\u548c\u767e\u5206\u4e4b\u4e03\u5341\u4e00\u70b9\u56db\u4e09\u3002<\/p>\n
samtools view -b -F 4 \\\r\n  -o mapped_only.bam all_reads.bam\r\n<\/code><\/pre>\n
\u4ece\u8f93\u5165\u6587\u4ef6\u7684\u89d2\u5ea6\u770b\uff0c\u5206\u6bcd\u5df2\u7ecf\u53ea\u5269\u4e0b\u5df2\u6bd4\u5bf9\u8bfb\u6bb5\u3002\u5bf9\u4e8e CoverM \u80fd\u770b\u5230\u7684\u8fd9\u4e9b\u8bb0\u5f55\uff0c\u5168\u90e8\u90fd\u6709\u6bd4\u5bf9\u4f4d\u7f6e\uff0c\u6240\u4ee5\u672a\u6bd4\u5bf9\u884c\u62a5\u544a\u4e3a\u96f6\uff0c\u4e24\u4e2a\u57fa\u56e0\u7ec4\u7684\u76f8\u5bf9\u4e30\u5ea6\u52a0\u8d77\u6765\u4e3a\u767e\u5206\u4e4b\u767e\u3002<\/p>\n
\u5982\u679c\u4e0d\u540c\u6279\u6b21\u4e2d\uff0c\u6709\u4e9b\u6587\u4ef6\u4fdd\u7559\u672a\u6bd4\u5bf9\u8bb0\u5f55\uff0c\u6709\u4e9b\u6587\u4ef6\u5df2\u7ecf\u505a\u8fc7\u7c7b\u4f3c\u8fc7\u6ee4\uff0c\u518d\u628a\u4e30\u5ea6\u8868\u76f4\u63a5\u5408\u5e76\uff0c\u5f97\u5230\u7684\u5dee\u5f02\u53ef\u80fd\u540c\u65f6\u5305\u542b\u6587\u4ef6\u5904\u7406\u65b9\u5f0f\u7684\u5f71\u54cd\u3002\u5f00\u59cb\u591a\u6837\u672c\u6bd4\u8f83\u4e4b\u524d\uff0c\u53ef\u4ee5\u5148\u6838\u5bf9\u6bcf\u4efd BAM \u7684\u603b\u8bb0\u5f55\u6570\u3001\u5df2\u6bd4\u5bf9\u8bb0\u5f55\u6570\u548c\u539f\u59cb\u6d4b\u5e8f\u8bfb\u6bb5\u7edf\u8ba1\uff0c\u660e\u786e\u4e30\u5ea6\u6240\u4f7f\u7528\u7684\u5206\u6bcd\u3002<\/p>\n
\u4e5f\u5e94\u6ce8\u610f\uff0c\u672c\u4f8b\u91c7\u7528\u5355\u7aef\u3001\u5355\u4e00\u4e3b\u6bd4\u5bf9\u8bb0\u5f55\u3002\u771f\u5b9e\u53cc\u7aef\u6570\u636e\u4ee5\u53ca\u5305\u542b\u6b21\u7ea7\u3001\u8865\u5145\u6bd4\u5bf9\u7684\u6587\u4ef6\uff0c\u9700\u8981\u4f9d\u636e\u5b9e\u9645\u8fc7\u6ee4\u89c4\u5219\u6838\u5bf9\u8bfb\u6bb5\u548c\u8bb0\u5f55\u7684\u5bf9\u5e94\u5173\u7cfb\u3002\u628a\u8f93\u5165\u9650\u5b9a\u6761\u4ef6\u5199\u5165\u5206\u6790\u8bb0\u5f55\uff0c\u53ef\u4ee5\u5e2e\u52a9\u540e\u7eed\u590d\u67e5\u8ba1\u6570\u5dee\u5f02\u6765\u81ea\u54ea\u91cc\u3002<\/p>\n
\u4e00\u4e2a\u5b9e\u8dd1\u4e2d\u9047\u5230\u7684\u53c2\u6570\u7ec4\u5408\u95ee\u9898<\/h2>\n
\u672c\u6b21\u8fd8\u5c1d\u8bd5\u628a\u8bfb\u6bb5\u8ba1\u6570\u4e0e\u5e73\u5747\u6df1\u5ea6\u653e\u5728\u540c\u4e00\u6761\u547d\u4ee4\u91cc\u8f93\u51fa\u3002\u5f53\u6700\u5c0f\u8986\u76d6\u5e7f\u5ea6\u5927\u4e8e\u96f6\u65f6\uff0c\u672c\u6b21\u7248\u672c\u660e\u786e\u62a5\u9519\uff0c\u63d0\u793a\u8ba1\u6570\u4f30\u8ba1\u5668\u4e0d\u8ba1\u7b97\u8986\u76d6\u5e7f\u5ea6\uff0c\u56e0\u6b64\u4e0d\u80fd\u4e0e\u8fd9\u4e2a\u95e8\u69db\u7ec4\u5408\u4f7f\u7528\u3002<\/p>\n
\u5904\u7406\u65b9\u5f0f\u662f\u628a\u539f\u59cb\u8bfb\u6bb5\u8ba1\u6570\u53e6\u884c\u8ba1\u7b97\uff0c\u5728\u8ba1\u6570\u547d\u4ee4\u4e2d\u5c06\u6700\u5c0f\u8986\u76d6\u5e7f\u5ea6\u8bbe\u4e3a\u96f6\u3002\u5b9e\u9645\u5f97\u5230\u7532\u5341\u6761\u3001\u4e59\u4e94\u5341\u6761\uff0c\u4e0e\u8f93\u5165\u8bbe\u8ba1\u5b8c\u5168\u4e00\u81f4\u3002\u8fd9\u6837\u53ef\u4ee5\u540c\u65f6\u4fdd\u7559\u539f\u59cb\u8ba1\u6570\u548c\u7ecf\u8fc7\u5e7f\u5ea6\u6761\u4ef6\u7b5b\u9009\u7684\u4e30\u5ea6\u8868\uff0c\u540e\u7eed\u518d\u6309\u57fa\u56e0\u7ec4\u540d\u79f0\u8fde\u63a5\u3002<\/p>\n
coverm genome \\\r\n  --bam-files all_reads.bam \\\r\n  --genome-definition genomes.tsv \\\r\n  --methods count \\\r\n  --min-covered-fraction 0 \\\r\n  --output-file read_counts.tsv\r\n<\/code><\/pre>\n
\u5c06\u4e24\u5f20\u8868\u5408\u5e76\u65f6\uff0c\u5efa\u8bae\u7ed9\u5b57\u6bb5\u6ce8\u660e\u8ba1\u7b97\u6761\u4ef6\u3002\u67d0\u4e2a\u57fa\u56e0\u7ec4\u539f\u59cb\u8ba1\u6570\u5927\u4e8e\u96f6\u3001\u7b5b\u9009\u540e\u7684\u5e73\u5747\u6df1\u5ea6\u5374\u4e3a\u96f6\uff0c\u5728\u672c\u6b21\u5b9e\u9a8c\u91cc\u5b8c\u5168\u53ef\u4ee5\u89e3\u91ca\u3002\u82e5\u53ea\u4fdd\u7559\u6700\u540e\u4e00\u5f20\u8868\uff0c\u5c31\u4f1a\u5931\u53bb\u8ffd\u8e2a\u5c40\u90e8\u652f\u6301\u4fe1\u53f7\u7684\u7ebf\u7d22\u3002<\/p>\n
\u8fd8\u53ef\u4ee5\u7528\u4e00\u4e2a\u72ec\u7acb\u7684\u9010\u4f4d\u70b9\u7edf\u8ba1\u6765\u6838\u5bf9\u6c47\u603b\u503c\u3002\u672c\u6b21\u8865\u8dd1\u4e86\u4e0b\u9762\u7684\u547d\u4ee4\uff0c\u8981\u6c42\u628a\u96f6\u8986\u76d6\u4f4d\u7f6e\u4e5f\u8f93\u51fa\u3002\u7532\u5f97\u5230\u4e00\u5343\u4e2a\u4f4d\u70b9\uff0c\u6df1\u5ea6\u603b\u548c\u4e3a\u4e00\u5343\uff0c\u6240\u6709\u4f4d\u7f6e\u5747\u6709\u8986\u76d6\u3002\u4e59\u5f97\u5230\u4e24\u5343\u4e2a\u4f4d\u70b9\uff0c\u6df1\u5ea6\u603b\u548c\u4e3a\u4e94\u5343\uff0c\u5176\u4e2d\u53ea\u6709\u4e00\u767e\u4e2a\u4f4d\u70b9\u5f97\u5230\u8986\u76d6\uff0c\u6700\u9ad8\u4f4d\u70b9\u6df1\u5ea6\u4e3a\u4e94\u5341\u3002\u7531\u8fd9\u4e9b\u9010\u4f4d\u70b9\u6570\u503c\u91cd\u65b0\u6c42\u5e73\u5747\uff0c\u53ef\u4ee5\u518d\u6b21\u5f97\u5230\u524d\u9762\u7684\u6df1\u5ea6\u548c\u5e7f\u5ea6\u3002<\/p>\n
samtools depth -aa all_reads.bam > per_base_depth.tsv\r\n<\/code><\/pre>\n
\u9010\u4f4d\u70b9\u7ed3\u679c\u8fd8\u80fd\u5e2e\u52a9\u5224\u65ad\u8986\u76d6\u662f\u5426\u96c6\u4e2d\u3002\u4e24\u4e2a\u53c2\u8003\u5373\u4f7f\u62e5\u6709\u76f8\u540c\u7684\u5e73\u5747\u6df1\u5ea6\uff0c\u4e5f\u53ef\u80fd\u5206\u522b\u5bf9\u5e94\u5747\u5300\u8986\u76d6\u4e0e\u5c40\u90e8\u9ad8\u5cf0\u3002\u5b9e\u9645\u6392\u67e5\u65f6\uff0c\u53ef\u4ee5\u6309\u7a97\u53e3\u6c47\u603b\u6df1\u5ea6\uff0c\u67e5\u770b\u4fe1\u53f7\u662f\u5426\u96c6\u4e2d\u5728\u5c11\u6570\u4fdd\u5b88\u57fa\u56e0\u3001\u91cd\u590d\u533a\u57df\u6216\u7247\u6bb5\u672b\u7aef\uff0c\u5e76\u4e0e\u76f8\u5173\u533a\u57df\u7684\u5e8f\u5217\u6ce8\u91ca\u5bf9\u5e94\u8d77\u6765\u3002<\/p>\n
\u5c55\u793a\u7ed3\u679c\u65f6\u8fd8\u5e94\u533a\u5206\u5c0f\u6570\u4e0e\u767e\u5206\u6570\u3002\u8986\u76d6\u5e7f\u5ea6\u5217\u4e2d\u7684\u96f6\u70b9\u96f6\u4e94\u5bf9\u5e94\u767e\u5206\u4e4b\u4e94\uff0c\u76f8\u5bf9\u4e30\u5ea6\u5217\u5df2\u7ecf\u4ee5\u767e\u5206\u6570\u62a5\u544a\u3002\u7a0b\u5e8f\u8f93\u51fa\u7684\u672a\u6bd4\u5bf9\u6bd4\u4f8b\u6709\u65f6\u4f1a\u663e\u793a\u4e3a\u4e09\u5341\u4e5d\u70b9\u4e5d\u4e5d\u4e5d\u4e5d\u4e5d\u516d\uff0c\u8fd9\u662f\u6d6e\u70b9\u6570\u8868\u793a\u9020\u6210\u7684\u5fae\u5c0f\u5dee\u5f02\u3002\u8868\u683c\u5c55\u793a\u65f6\u53ef\u4ee5\u5408\u7406\u56db\u820d\u4e94\u5165\uff0c\u8fdb\u884c\u81ea\u52a8\u6838\u5bf9\u65f6\u5219\u4f7f\u7528\u9002\u5f53\u5bb9\u5dee\uff0c\u540c\u65f6\u4fdd\u7559\u539f\u59cb\u8f93\u51fa\u4ee5\u4fbf\u8ffd\u6eaf\u3002<\/p>\n
\u8fc1\u79fb\u5230\u771f\u5b9e\u6570\u636e\u65f6\uff0c\u600e\u6837\u9010\u9879\u6838\u5bf9<\/h2>\n
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