{"id":70904,"date":"2026-11-15T00:06:49","date_gmt":"2026-11-14T16:06:49","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70904"},"modified":"2026-11-15T00:06:49","modified_gmt":"2026-11-14T16:06:49","slug":"canu-hifi-unassembled-contigs-overlap-covered-length","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/canu-hifi-unassembled-contigs-overlap-covered-length\/","title":{"rendered":"Canu \u5b9e\u8dd1\uff5c\u4e3b\u7ec4\u88c5\u91cc\u627e\u4e0d\u5230\u7684 18 kb\uff0c\u4e3a\u4ec0\u4e48\u8fd8\u80fd\u5728\u4e09\u4e2a\u672a\u7ec4\u88c5\u7247\u6bb5\u91cc\u5168\u90e8\u627e\u56de\uff1f"},"content":{"rendered":"
\n

\u4e00\u4efd\u7ec4\u88c5\u4ea4\u4ed8\u7269\u6709\u4e24\u4e2a FASTA\u3002\u4e3b\u7ed3\u679c\u53ea\u6709\u516b\u4e07\u78b1\u57fa\uff0c\u800c\u8f93\u5165\u6837\u672c\u660e\u660e\u8fd8\u6709\u4e00\u6bb5\u4e00\u4e07\u516b\u5343\u78b1\u57fa\u7684\u6a21\u677f\u3002\u53e6\u4e00\u4e2a\u6587\u4ef6\u6807\u7740\u672a\u7ec4\u88c5\uff0c\u91cc\u9762\u4e09\u6bb5\u957f\u5ea6\u76f8\u52a0\u5374\u6709\u4e24\u4e07\u516d\u5343\u591a\u3002\u5355\u770b\u4efb\u4f55\u4e00\u4e2a\u6570\u5b57\u90fd\u5f88\u96be\u89e3\u91ca\u3002\u6211\u4eec\u5b9e\u9645\u8fd0\u884c Canu \u7684\u9ad8\u51c6\u786e\u957f\u8bfb\u6bb5\u6a21\u5f0f\uff0c\u8ffd\u8e2a\u6bcf\u4e2a\u7247\u6bb5\u7528\u4e86\u591a\u5c11\u6761\u8bfb\u6bb5\uff0c\u53d6\u5f97\u5171\u8bc6\u524d\u540e\u7684\u4e24\u9636\u6bb5\u62a5\u544a\uff0c\u5e76\u628a\u7ed3\u679c\u6bd4\u56de\u5df2\u77e5\u6a21\u677f\u3002\u539f\u6765\u201c\u8fd9\u6bb5\u5e8f\u5217\u6709\u8bc1\u636e\u201d\u201c\u8fd9\u6bb5\u88ab\u7ec4\u88c5\u6210\u4e00\u4e2a\u8fde\u7eed\u5206\u5b50\u201d\u548c\u201c\u8fd9\u6bb5\u88ab\u7eb3\u5165\u4e3b\u7ed3\u679c\u201d\u80fd\u6709\u4e09\u4e2a\u4e0d\u540c\u7b54\u6848\u3002Canu \u5b98\u65b9\u5206\u6790\u6559\u7a0b<\/a><\/p>\n

\u8ba9\u540c\u4e00\u6837\u672c\u91cc\u540c\u65f6\u51fa\u73b0\u6df1\u8986\u76d6\u548c\u6d45\u8986\u76d6<\/h2>\n

\u751f\u6210\u4e24\u6761\u7ebf\u6027\u968f\u673a\u5e8f\u5217\uff0c\u5927\u7684\u4e00\u6761\u957f\u516b\u4e07\uff0c\u5c0f\u7684\u4e00\u6761\u957f\u4e00\u4e07\u516b\u5343\u3002\u957f\u6a21\u677f\u62bd\u53d6\u56db\u767e\u4e8c\u5341\u6761\u65e0\u9519\u957f\u8bfb\u6bb5\uff0c\u9664\u5c11\u91cf\u8bfb\u6bb5\u56fa\u5b9a\u89e6\u53ca\u4e24\u7aef\uff0c\u5176\u4f59\u8d77\u70b9\u968f\u673a\u3002\u77ed\u6a21\u677f\u53ea\u53d6\u4e03\u6761\uff0c\u6bcf\u6761\u4ecd\u6709\u4e94\u5343\u5230\u516d\u5343\u516b\u767e\u4e2a\u78b1\u57fa\uff0c\u8d77\u70b9\u6cbf\u6a21\u677f\u5206\u5f00\u6446\u653e\uff0c\u9996\u5c3e\u90fd\u6709\u4eba\u8986\u76d6\uff0c\u4e2d\u95f4\u7247\u6bb5\u6709\u91cd\u53e0\u3002\u4e24\u4efd\u8bfb\u6bb5\u5408\u5e76\u540e\u4e00\u8d77\u7ec4\u88c5\uff0c\u7a0b\u5e8f\u6ca1\u6709\u5f97\u5230\u6a21\u677f\u8eab\u4efd\u6216\u5e8f\u5217\u3002\u8fd9\u4e2a\u6a21\u578b\u6545\u610f\u628a\u5c0f\u6a21\u677f\u653e\u5728\u5f88\u4f4e\u7684\u5c40\u90e8\u6df1\u5ea6\uff0c\u7814\u7a76\u7684\u662f\u8986\u76d6\u4e0d\u8db3\u65f6\u4ea7\u7269\u5982\u4f55\u5206\u7c7b\u3002\u5b83\u6ca1\u6709\u6a21\u62df\u566a\u58f0\u3001\u590d\u6742\u91cd\u590d\u548c\u6df7\u6837\uff0c\u4e0d\u80fd\u76f4\u63a5\u56de\u7b54\u5b9e\u9645\u7fa4\u843d\u91cc\u7a00\u6709\u6210\u5458\u7684\u68c0\u51fa\u7387\u3002<\/p>\n

Canu 2.2 \u4f7f\u7528\u9ad8\u51c6\u786e\u6a21\u5f0f\u3001\u76f8\u540c\u7684\u6700\u77ed\u8bfb\u957f\u548c\u6700\u5c0f\u91cd\u53e0\u8bbe\u7f6e\u8fd0\u884c\u3002\u8bbe\u5b9a\u7684\u57fa\u56e0\u7ec4\u5927\u5c0f\u662f\u4e24\u6761\u6a21\u677f\u7684\u957f\u5ea6\u4e4b\u548c\u3002\u4efb\u52a1\u6210\u529f\u7ed3\u675f\u540e\uff0c\u5148\u4fdd\u5b58\u9636\u6bb5\u62a5\u544a\u3001\u4e3b\u5171\u8bc6\u3001\u672a\u7ec4\u88c5\u6587\u4ef6\u548c\u7247\u6bb5\u5e03\u5c40\u8868\uff0c\u518d\u770b\u662f\u5426\u51fa\u73b0\u76ee\u6807\u5e8f\u5217\u3002\u5982\u679c\u53ea\u4ea4\u63a5\u4e3b FASTA\uff0c\u7a00\u5c11\u6a21\u677f\u7684\u8bc1\u636e\u4f1a\u6574\u4e2a\u9000\u51fa\u540e\u7eed\u68c0\u7d22\u3002\u5982\u679c\u987a\u624b\u628a\u4e24\u4efd FASTA \u62fc\u8d77\u6765\u91cd\u65b0\u62a5\u603b\u957f\u5ea6\uff0c\u53c8\u4f1a\u628a\u91cd\u590d\u8986\u76d6\u540c\u4e00\u4f4d\u7f6e\u7684\u4e09\u4e2a\u7247\u6bb5\u5f53\u6210\u4e92\u4e0d\u91cd\u53e0\u7684\u533a\u57df\u3002\u9009\u62e9\u4ea4\u4ed8\u54ea\u4e2a\u6587\u4ef6\u53d6\u51b3\u4e8e\u95ee\u9898\u662f\u51c6\u5907\u6ce8\u91ca\u4e3b\u7ec4\u88c5\uff0c\u8fd8\u662f\u5bfb\u627e\u4f4e\u8986\u76d6\u76ee\u6807\u7684\u7ebf\u7d22\u3002Canu \u5feb\u901f\u4e0a\u624b\u4e0e\u8f93\u5165\u7c7b\u578b<\/a><\/p>\n

\u4e09\u4e2a\u7247\u6bb5\u600e\u6837\u8986\u76d6\u540c\u4e00\u4e2a\u77ed\u6a21\u677f<\/h2>\n

\u4e3b\u6587\u4ef6\u5f97\u5230\u4e00\u6761\u516b\u4e07\u78b1\u57fa\u7684\u7247\u6bb5\uff0c\u6807\u9898\u8bb0\u5f55\u7528\u4e86\u56db\u767e\u4e8c\u5341\u6761\u8bfb\u6bb5\u3002\u6bd4\u56de\u957f\u6a21\u677f\u65f6\u516b\u4e07\u4e2a\u5bf9\u9f50\u5217\u5168\u90e8\u4e00\u81f4\uff0c\u5e03\u5c40\u8868\u7ed9\u51fa\u7684\u8986\u76d6\u503c\u7ea6\u4e3a\u4e09\u5341\u4e00\u70b9\u4e94\u4e5d\u3002\u77ed\u6a21\u677f\u6ca1\u6709\u51fa\u73b0\u5728\u4e3b\u6587\u4ef6\uff0c\u5374\u5728\u672a\u7ec4\u88c5\u6587\u4ef6\u4e2d\u4ea7\u751f\u4e09\u4e2a\u6761\u76ee\u3002\u6700\u957f\u8005\u4e3a\u4e00\u4e07\u56db\u5343\u96f6\u56db\u5341\u4e94\u4e2a\u78b1\u57fa\uff0c\u6807\u9898\u6807\u660e\u4e94\u6761\u8bfb\u6bb5\u3002\u53e6\u4e24\u6761\u5404\u53ea\u6709\u4e00\u6761\u8bfb\u6bb5\uff0c\u5404\u957f\u516d\u5343\u4e03\u767e\u96f6\u4e5d\u548c\u4e94\u5343\u4e09\u767e\u516d\u5341\u4e5d\u3002\u7531\u6b64\u53ef\u4ee5\u5148\u505a\u4e00\u6b21\u8ba1\u6570\u6838\u5bf9\uff0c\u4e94\u52a0\u4e00\u52a0\u4e00\u6070\u597d\u5bf9\u5e94\u7ed9\u77ed\u6a21\u677f\u8bbe\u8ba1\u7684\u4e03\u6761\u8bfb\u6bb5\u3002\u4f46\u4e00\u4e2a\u6587\u4ef6\u88ab\u79f0\u4e3a\u672a\u7ec4\u88c5\uff0c\u5e76\u4e0d\u610f\u5473\u7740\u91cc\u9762\u6bcf\u4e00\u884c\u5e8f\u5217\u90fd\u53ea\u7531\u4e00\u6761\u8bfb\u6bb5\u6784\u6210\u3002<\/p>\n

\u628a\u4e09\u6bb5\u90fd\u5bf9\u56de\u77ed\u6a21\u677f\uff0c\u6309\u96f6\u57fa\u5de6\u95ed\u53f3\u5f00\u533a\u95f4\u5206\u522b\u5f97\u5230 1995 \u81f3 16040\u30010 \u81f3 6709\u300112631 \u81f3 18000\u3002\u5148\u6309\u8d77\u70b9\u6392\u5e8f\u518d\u5408\u5e76\u533a\u95f4\uff0c\u9996\u5c3e\u76f8\u63a5\u8986\u76d6\u4ece\u96f6\u5230\u4e00\u4e07\u516b\u5343\u7684\u5168\u90e8\u4f4d\u7f6e\u3002\u539f\u59cb\u957f\u5ea6\u76f4\u63a5\u76f8\u52a0\u5374\u662f\u4e8c\u4e07\u516d\u5343\u4e00\u767e\u4e8c\u5341\u4e09\uff0c\u591a\u51fa\u7684\u516b\u5343\u4e00\u767e\u4e8c\u5341\u4e09\u6765\u81ea\u533a\u95f4\u4e4b\u95f4\u7684\u91cd\u53e0\u3002\u5373\u4f7f\u6bcf\u6bb5\u5728\u5bf9\u5e94\u6a21\u677f\u4e0a\u7684\u78b1\u57fa\u90fd\u5b8c\u5168\u6b63\u786e\uff0c\u4e5f\u53ea\u80fd\u8bf4\u5df2\u77e5\u6a21\u677f\u4e0a\u7684\u6bcf\u4e2a\u4f4d\u7f6e\u5728\u81f3\u5c11\u4e00\u4e2a\u7247\u6bb5\u4e2d\u627e\u5f97\u5230\uff0c\u5e76\u6ca1\u6709\u4e00\u6761\u5b9e\u9645\u8f93\u51fa\u7684\u5e8f\u5217\u72ec\u7acb\u8986\u76d6\u5168\u957f\u3002\u5728\u6ca1\u6709\u771f\u503c\u7684\u6837\u672c\u91cc\uff0c\u8fd9\u4e2a\u533a\u522b\u66f4\u91cd\u8981\uff0c\u5c24\u5176\u4e0d\u80fd\u6839\u636e\u67d0\u4e2a\u8fd1\u7f18\u53c2\u8003\u64c5\u81ea\u586b\u8865\u4e24\u4e2a\u7247\u6bb5\u4e4b\u95f4\u7684\u8fde\u63a5\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u672a\u7ec4\u88c5\u6587\u4ef6\u91cc\u7684\u7247\u6bb5<\/th>\n\u957f\u5ea6<\/th>\n\u8bfb\u6bb5\u6570<\/th>\n\u77ed\u6a21\u677f\u96f6\u57fa\u533a\u95f4<\/th>\n<\/tr>\n<\/thead>\n
\u4e2d\u6bb5<\/td>\n14045 bp<\/td>\n5<\/td>\n[1995, 16040)<\/td>\n<\/tr>\n
\u5de6\u7aef<\/td>\n6709 bp<\/td>\n1<\/td>\n[0, 6709)<\/td>\n<\/tr>\n
\u53f3\u7aef<\/td>\n5369 bp<\/td>\n1<\/td>\n[12631, 18000)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"18
\u4e00\u4e2a\u4f4e\u8986\u76d6\u6a21\u677f\u88ab\u5206\u5230\u4e09\u4e2a\u672a\u7ec4\u88c5\u7247\u6bb5\uff0c\u7528\u533a\u95f4\u5e76\u96c6\u6838\u5bf9\u4e22\u5931\u4e0e\u91cd\u53e0\u3002<\/figcaption><\/figure>\n

\u5b9e\u9645\u5236\u4f5c\u7edf\u8ba1\u8868\u65f6\u6700\u597d\u5355\u5217\u7247\u6bb5\u8986\u76d6\u6a21\u677f\u7684\u6bd4\u4f8b\u3001\u6a21\u677f\u88ab\u6240\u6709\u7247\u6bb5\u8986\u76d6\u7684\u6bd4\u4f8b\u53ca\u6700\u957f\u8fde\u7eed\u7247\u6bb5\u957f\u5ea6\u3002\u7b2c\u4e00\u9879\u5bf9\u6bcf\u6761\u8f93\u51fa\u8ba1\u7b97\uff0c\u7b2c\u4e8c\u9879\u5148\u5408\u5e76\u91cd\u53e0\uff0c\u6700\u540e\u4e00\u9879\u76f4\u63a5\u4ece\u5355\u6761\u5e8f\u5217\u8bfb\u53d6\u3002\u4e09\u4e2a\u6307\u6807\u653e\u5728\u4e00\u884c\uff0c\u5c31\u80fd\u89e3\u91ca\u4e3a\u4ec0\u4e48\u4e00\u4e2a\u6a21\u677f\u53ef\u4ee5\u8986\u76d6\u767e\u5206\u4e4b\u767e\uff0c\u540c\u65f6\u4ecd\u7f3a\u5c11\u4e00\u6761\u5168\u957f\u7ec4\u88c5\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u540c\u4e00\u4efd\u62a5\u544a\u4e5f\u53ef\u80fd\u6709\u4e24\u79cd\u957f\u5ea6\u5355\u4f4d\u80cc\u666f<\/h2>\n
canu -p mini -d asm genomeSize=98k useGrid=false maxThreads=4 maxMemory=8 minReadLength=1000 minOverlapLength=1000 -pacbio-hifi reads.fa\r\ngrep '^>' asm\/mini.contigs.fasta asm\/mini.unassembled.fasta\r\nminimap2 -x asm5 -c --secondary=no ref.fa asm\/mini.unassembled.fasta > short.paf\r\ncut -f1,6,8,9,10,11 short.paf\r\n<\/code><\/pre>\n
\u9636\u6bb5\u62a5\u544a\u4e2d\u8fd8\u6709\u4e00\u4e2a\u503c\u5f97\u5355\u72ec\u6838\u5bf9\u7684\u5dee\u5f02\u3002\u4e3b\u7247\u6bb5\u5728\u6784\u5efa\u5b8c\u6210\u3001\u751f\u6210\u6700\u7ec8\u5171\u8bc6\u4e4b\u524d\u957f\u4e94\u4e07\u4e5d\u5343\u516b\u767e\u4e03\u5341\u4e5d\uff0c\u5171\u8bc6\u4e4b\u540e\u957f\u516b\u4e07\u3002\u672a\u7ec4\u88c5\u90e8\u5206\u4e5f\u7531\u4e00\u4e07\u4e5d\u5343\u516d\u767e\u516d\u5341\u53d8\u4e3a\u4e8c\u4e07\u516d\u5343\u4e00\u767e\u4e8c\u5341\u4e09\uff0c\u4e24\u8f6e\u7684\u8bb0\u5f55\u6570\u5374\u90fd\u76f8\u540c\u3002\u5b98\u65b9\u6587\u6863\u7279\u522b\u6307\u51fa\uff0c\u9ad8\u51c6\u786e\u8bfb\u6bb5\u6a21\u5f0f\u5728\u5171\u8bc6\u4e4b\u524d\u4ee5\u540c\u805a\u7269\u538b\u7f29\u540e\u7684\u5e8f\u5217\u7a7a\u95f4\u62a5\u544a\u7edf\u8ba1\u3002\u591a\u4e2a\u8fde\u7eed\u76f8\u540c\u7684\u5b57\u6bcd\u53ef\u4ee5\u4e34\u65f6\u8868\u793a\u6210\u4e00\u4e2a\u5355\u4f4d\u3002\u62ff\u65e9\u671f\u9636\u6bb5\u7684\u6570\u5b57\u76f4\u63a5\u548c\u6700\u7ec8\u4ea7\u7269\u4f5c\u5dee\uff0c\u518d\u628a\u5dee\u503c\u89e3\u91ca\u6210\u540e\u7eed\u627e\u56de\u7684\u57fa\u56e0\u533a\u6bb5\uff0c\u4f1a\u6df7\u6dc6\u5750\u6807\u7a7a\u95f4\u3002\u9a8c\u6536\u65f6\u8981\u6284\u4e0b\u9636\u6bb5\u6807\u9898\uff0c\u5e76\u5c3d\u91cf\u4ece\u6700\u7ec8 FASTA \u76f4\u63a5\u590d\u7b97\u4e00\u6b21\u957f\u5ea6\u3002Canu \u5bf9\u9636\u6bb5\u7edf\u8ba1\u4e0e\u540c\u805a\u7269\u538b\u7f29\u7684\u8bf4\u660e<\/a><\/p>\n
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