{"id":71176,"date":"2026-11-15T00:15:03","date_gmt":"2026-11-14T16:15:03","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71176"},"modified":"2026-11-15T00:15:03","modified_gmt":"2026-11-14T16:15:03","slug":"verkko-gaf-node-coverage-fractional-alignment-rows","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/verkko-gaf-node-coverage-fractional-alignment-rows\/","title":{"rendered":"Verkko \u7ec4\u88c5\u56fe\u5b9e\u64cd\uff5c\u540c\u4e00\u4e2a\u8282\u70b9\u6709 3 \u500d\u8986\u76d6\uff0c\u4e3a\u4ec0\u4e48\u62ff\u6389\u4e00\u884c\u6bd4\u5bf9\u5c31\u5269 2.5 \u500d\uff1f"},"content":{"rendered":"
\n

\u62ff\u5230\u4e00\u5f20\u7ec4\u88c5\u56fe\uff0c\u770b\u5230\u4e00\u4e2a\u8282\u70b9\u6807\u7740\u4e09\u500d\u8986\u76d6\uff0c\u6700\u81ea\u7136\u7684\u8ffd\u95ee\u662f\u6709\u51e0\u6761\u5206\u5b50\u7ecf\u8fc7\u5b83\u3002\u4e24\u4e2a\u6570\u5b57\u4e4b\u95f4\u5e76\u6ca1\u6709\u7b80\u5355\u7684\u4e00\u4e00\u5bf9\u5e94\u3002\u4e00\u4e2a\u6bd4\u5bf9\u53ef\u4ee5\u53ea\u8d70\u8fc7\u8282\u70b9\u7684\u4e00\u534a\uff0c\u4e00\u6761\u8bfb\u6bb5\u4e5f\u53ef\u4ee5\u6709\u591a\u6761\u5019\u9009\u6bd4\u5bf9\u3002Verkko \u7684\u56fe\u5904\u7406\u5de5\u5177\u91cc\u6709\u4e00\u4e2a\u5f88\u77ed\u7684\u8986\u76d6\u8ba1\u7b97\u811a\u672c\uff0c\u6b63\u9002\u5408\u628a\u8fd9\u4e24\u4e2a\u95ee\u9898\u62c6\u5f00\u6838\u7b97\u3002\u6211\u4eec\u53d6\u5b98\u65b9\u53d1\u5e03\u7684 2.3.2 \u7248\uff0c\u5728\u672c\u5730\u5b9e\u9645\u8fd0\u884c\u5176\u4e2d\u7684\u8282\u70b9\u8986\u76d6\u8ba1\u7b97\u7ec4\u4ef6\uff0c\u7528\u4e00\u4e2a\u53ef\u4ee5\u624b\u7b97\u7684\u56fe\u4e0e\u4e94\u884c\u8def\u5f84\u6bd4\u5bf9\u5f97\u5230\u4e0b\u9762\u7684\u7ed3\u679c\u3002\u6b64\u6b21\u5b9e\u9a8c\u4ece\u5df2\u6709\u56fe\u548c\u6bd4\u5bf9\u5f00\u59cb\uff0c\u9a8c\u8bc1\u7684\u8303\u56f4\u662f\u8fd9\u4e00\u9879\u7edf\u8ba1\u3002Verkko \u7248\u672c\u4e0e\u8f93\u5165\u8f93\u51fa\u8bf4\u660e<\/a><\/p>\n

\u5148\u628a\u56fe\u4e0a\u8def\u5f84\u753b\u6210\u6709\u957f\u5ea6\u7684\u5750\u6807\u8f74<\/h2>\n

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\u7b2c\u4e8c\u6761\u8bfb\u6bb5\u4ece\u76f8\u53cd\u65b9\u5411\u8d70\u540c\u4e00\u7ec4\u8282\u70b9\u3002\u8def\u5f84\u7684\u8d77\u70b9\u53d8\u6210\u4e94\u5341\u78b1\u57fa\u8282\u70b9\u7684\u53e6\u4e00\u5934\uff0c\u6cbf\u8fd9\u4e2a\u65b9\u5411\u4ece\u4e8c\u5341\u8d70\u5230\u4e09\u767e\u4e00\u5341\uff0c\u4ecd\u7136\u8986\u76d6\u4e24\u4e2a\u7aef\u70b9\u5404\u81ea\u7684\u516d\u6210\u3002\u82e5\u770b\u89c1\u53cd\u5411\u6807\u8bb0\u5c31\u76f4\u63a5\u628a\u7b2c\u4e00\u6761\u8def\u5f84\u7684\u8d77\u6b62\u6570\u5b57\u539f\u6837\u6284\u8fc7\u53bb\uff0c\u4f1a\u9519\u7f6e\u526a\u88c1\u7684\u65b9\u5411\u3002\u5728\u56fe\u4e0a\u627e\u5230\u8def\u5f84\u9996\u8282\u70b9\u548c\u5c3e\u8282\u70b9\uff0c\u6309\u7167\u884c\u8fdb\u65b9\u5411\u7b97\u5269\u4e0b\u591a\u5c11\u78b1\u57fa\uff0c\u518d\u4ee5\u4e0d\u5e26\u65b9\u5411\u7684\u8282\u70b9\u540d\u6c47\u603b\uff0c\u7b2c\u4e8c\u6761\u7684\u8d21\u732e\u6070\u597d\u4e0e\u7b2c\u4e00\u6761\u76f8\u540c\u3002\u56fe\u7684\u8282\u70b9\u6df1\u5ea6\u56e0\u6b64\u53ef\u4ee5\u51fa\u73b0\u5c0f\u6570\uff0c\u5373\u4f7f\u6d4b\u5e8f\u5206\u5b50\u7684\u6570\u91cf\u603b\u662f\u6574\u6570\u3002GAF \u8def\u5f84\u5750\u6807\u4e0e\u65b9\u5411\u5b57\u6bb5\u89c4\u8303<\/a><\/p>\n

\u63a5\u7740\u653e\u5165\u4e00\u6761\u53ea\u6bd4\u5230\u4e2d\u95f4\u8282\u70b9\u7684\u8bfb\u6bb5\u3002\u5b83\u5728\u4e8c\u767e\u4e2a\u78b1\u57fa\u91cc\u8986\u76d6\u4e86\u4e94\u5341\u5230\u4e00\u767e\u4e94\u5341\u8fd9\u4e00\u767e\u4e2a\u4f4d\u7f6e\uff0c\u8d21\u732e\u96f6\u70b9\u4e94\u3002\u4e3a\u6f14\u793a\u8bb0\u5f55\u7b5b\u9009\uff0c\u6211\u4eec\u4eba\u4e3a\u653e\u5165\u7b2c\u4e8c\u884c\u540c\u540d\u3001\u540c\u533a\u95f4\u7684\u6bd4\u5bf9\uff0c\u7ed9\u5b83\u7684\u6bd4\u5bf9\u8d28\u91cf\u8bbe\u4e3a\u96f6\uff0c\u539f\u6765\u7684\u90a3\u884c\u662f\u516d\u5341\u3002\u6700\u540e\u518d\u653e\u5165\u4e00\u6761\u5355\u72ec\u8986\u76d6\u7b2c\u4e09\u8282\u70b9\u5168\u957f\u7684\u8bfb\u6bb5\u3002\u6574\u4e2a\u6587\u4ef6\u4e2d\u53ea\u6709\u56db\u4e2a\u4e0d\u540c\u8bfb\u540d\uff0c\u5374\u6709\u4e94\u6761\u6570\u636e\u884c\u3002\u7b2c\u4e8c\u884c\u540c\u540d\u6bd4\u5bf9\u662f\u523b\u610f\u5236\u9020\u7684\u5bf9\u7167\uff0c\u5b9e\u9645\u9879\u76ee\u4e2d\u7684\u591a\u91cd\u6bd4\u5bf9\u8fd8\u53ef\u80fd\u51fa\u73b0\u5728\u4e0d\u540c\u8def\u5f84\u6216\u4e0d\u540c\u65b9\u5411\u4e0a\uff0c\u5e94\u6309\u81ea\u5df1\u7684\u5206\u6790\u76ee\u7684\u5b9a\u4e49\u53d6\u820d\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u8282\u70b9<\/th>\n\u957f\u5ea6<\/th>\n\u4e94\u884c\u5168\u90e8\u53c2\u4e0e<\/th>\n\u53bb\u6389\u4f4e\u8d28\u91cf\u884c<\/th>\n\u54ea\u4e9b\u6bd4\u5bf9\u8d21\u732e\u4e86\u8986\u76d6<\/th>\n<\/tr>\n<\/thead>\n
A<\/td>\n100<\/td>\n1.2<\/td>\n1.2<\/td>\n\u4e24\u4e2a\u7aef\u90e8\u8986\u76d6\u5404\u5360 0.6<\/td>\n<\/tr>\n
B<\/td>\n200<\/td>\n3.0<\/td>\n2.5<\/td>\n\u4e24\u6761\u8def\u5f84\u5168\u957f\u7ecf\u8fc7\uff0c\u52a0\u4e0a\u4e00\u884c\u6216\u4e24\u884c\u534a\u8282\u70b9\u547d\u4e2d<\/td>\n<\/tr>\n
C<\/td>\n50<\/td>\n2.2<\/td>\n2.2<\/td>\n\u4e24\u4e2a 0.6 \u4e0e\u4e00\u4e2a\u5168\u957f<\/td>\n<\/tr>\n
D<\/td>\n40<\/td>\n0.0<\/td>\n0.0<\/td>\n\u8282\u70b9\u5b58\u5728\uff0c\u8f93\u5165\u4e2d\u6ca1\u6709\u6bd4\u5bf9\u7ecf\u8fc7<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u8282\u70b9\u8986\u76d6\u600e\u6837\u7b97\u51fa
\u5728\u4e00\u4e2a\u53ef\u624b\u7b97\u7684\u5c0f\u56fe\u4e0a\uff0c\u5b9e\u9645\u8fd0\u884c Verkko \u7684\u8282\u70b9\u8986\u76d6\u8ba1\u7b97\u7ec4\u4ef6\u3002<\/figcaption><\/figure>\n

\u6838\u5bf9\u7ed3\u679c\u65f6\uff0c\u628a\u672a\u89c2\u5bdf\u5230\u7684\u8282\u70b9\u4e5f\u653e\u5728\u8868\u91cc\u3002\u7b2c\u56db\u4e2a\u8282\u70b9\u6709\u660e\u786e\u7684\u957f\u5ea6\u4e14\u51fa\u73b0\u5728\u56fe\u4e2d\uff0c\u6240\u4ee5\u8986\u76d6\u4e3a\u96f6\u6709\u53ef\u8ffd\u6eaf\u7684\u5206\u6bcd\u3002\u5982\u679c\u67d0\u8282\u70b9\u6839\u672c\u6ca1\u6709\u51fa\u73b0\u5728\u8fd9\u4e00\u7248\u56fe\u91cc\uff0c\u5de6\u8fde\u63a5\u540e\u5e94\u5148\u6807\u8bb0\u4e3a\u7f3a\u5931\uff0c\u4e0d\u80fd\u76f4\u63a5\u8865\u96f6\u5e76\u89e3\u91ca\u4e3a\u8fd9\u4e2a\u6837\u672c\u5728\u8be5\u533a\u57df\u6ca1\u6709\u8bfb\u6bb5\u3002\u4e24\u7248\u7ec4\u88c5\u5bf9\u9f50\u8282\u70b9\u540d\u65f6\u5c24\u5176\u5bb9\u6613\u6df7\u6dc6\u8fd9\u4e24\u79cd\u60c5\u51b5\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u53bb\u6389\u4e00\u884c\u540e\uff0c\u7528\u78b1\u57fa\u603b\u6570\u9a8c\u7b97<\/h2>\n
python3 calculate_coverage.py nodes.gfa < reads.gaf > all.tsv\r\nawk -F '\\t' '$12 >= 1' reads.gaf | python3 calculate_coverage.py nodes.gfa > filtered.tsv\r\ncat all.tsv\r\ncat filtered.tsv\r\n<\/code><\/pre>\n
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