{"id":70858,"date":"2026-11-15T00:05:14","date_gmt":"2026-11-14T16:05:14","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70858"},"modified":"2026-11-15T00:05:14","modified_gmt":"2026-11-14T16:05:14","slug":"hifiasm-haplotypes-duplicate-contigs-homozygous-coverage","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/hifiasm-haplotypes-duplicate-contigs-homozygous-coverage\/","title":{"rendered":"hifiasm \u5b9e\u8dd1\uff5c\u4e24\u5957\u7ec4\u88c5\u90fd\u957f\u4e86\u4e00\u500d\uff0c\u600e\u6837\u5224\u65ad\u5e8f\u5217\u62fc\u5bf9\u4e86\u3001\u5355\u500d\u578b\u5374\u5206\u9519\u4e86\uff1f"},"content":{"rendered":"
\n

\u62ff\u5230\u4e24\u4e2a\u5355\u500d\u578b\u6587\u4ef6\uff0c\u91cc\u9762\u90fd\u627e\u5230\u4e86\u5019\u9009\u57fa\u56e0\u7684\u4e24\u79cd\u7b49\u4f4d\u3002\u7814\u7a76\u4eba\u5458\u53ef\u80fd\u9a6c\u4e0a\u8ba8\u8bba\u57fa\u56e0\u52a0\u500d\uff0c\u4f46\u8fd8\u5b58\u5728\u53e6\u4e00\u79cd\u5f88\u5bb9\u6613\u9a8c\u8bc1\u7684\u89e3\u91ca\u3002\u4e24\u6761\u7b49\u4f4d\u5e8f\u5217\u90fd\u88ab\u6b63\u786e\u7ec4\u88c5\u51fa\u6765\uff0c\u968f\u540e\u5728\u5206\u914d\u5230\u4e24\u4e2a\u6587\u4ef6\u65f6\u5404\u4fdd\u7559\u4e86\u4e00\u4efd\u3002\u6211\u4eec\u7528\u4e24\u6761\u5df2\u77e5\u6a21\u677f\u5b9e\u8dd1 hifiasm\uff0c\u628a\u8f93\u51fa\u7684\u6bcf\u4e2a\u7247\u6bb5\u548c\u6a21\u677f\u9010\u78b1\u57fa\u6838\u5bf9\uff0c\u7136\u540e\u53ea\u6539\u53d8\u7eaf\u5408\u8986\u76d6\u53c2\u6570\u518d\u7ec4\u88c5\u4e00\u6b21\u3002\u4e24\u8f6e\u90fd\u627e\u56de\u5168\u90e8\u8bbe\u8ba1\u7684\u6807\u8bb0\uff0c\u53ea\u6709\u4e00\u8f6e\u628a\u4e24\u5957\u6807\u8bb0\u5206\u5230\u4e86\u4e0d\u540c\u6587\u4ef6\u3002\u8fd9\u4e2a\u533a\u522b\u51b3\u5b9a\u4e86\u4e0b\u6e38\u57fa\u56e0\u62f7\u8d1d\u6570\u5230\u5e95\u80fd\u4e0d\u80fd\u8fd9\u4e48\u6570\u3002hifiasm \u7248\u672c\u4e0e\u7528\u6cd5<\/a><\/p>\n

\u5206\u6e05\u4e24\u4e2a\u5c42\u7ea7\u7684\u6b63\u786e<\/h2>\n

\u5148\u751f\u6210\u4e00\u6761\u5341\u4e07\u78b1\u57fa\u7684\u5e8f\u5217\uff0c\u518d\u5728\u76f8\u9694\u4e8c\u767e\u4e8c\u5341\u4e03\u4e2a\u78b1\u57fa\u7684\u4f4d\u7f6e\u66ff\u6362\u4e00\u4e2a\u5b57\u6bcd\uff0c\u6784\u6210\u53e6\u4e00\u6761\u7b49\u957f\u6a21\u677f\u3002\u603b\u5171\u4e09\u767e\u516b\u5341\u516b\u4e2a\u5dee\u5f02\uff0c\u5176\u4ed6\u4f4d\u7f6e\u90fd\u76f8\u540c\u3002\u4e3a\u6bcf\u4e2a\u5dee\u5f02\u5728\u6bcf\u6761\u6a21\u677f\u4e0a\u5404\u53d6\u4e00\u4e2a\u4ee5\u5b83\u4e3a\u4e2d\u5fc3\u3001\u957f\u4e09\u5341\u4e00\u4e2a\u78b1\u57fa\u7684\u7a97\u53e3\uff0c\u5171\u4e24\u5957\u6807\u8bb0\u3002\u9010\u4e00\u9a8c\u8bc1\u6bcf\u4e2a\u6807\u8bb0\u53ca\u5176\u53cd\u5411\u4e92\u8865\u5728\u4e24\u6761\u6a21\u677f\u5408\u5728\u4e00\u8d77\u7684\u5e8f\u5217\u4e2d\u53ea\u5bf9\u5e94\u4e00\u4e2a\u4f4d\u7f6e\u3002\u5982\u6b64\u4e00\u6765\uff0c\u7ed3\u679c\u91cc\u540c\u65f6\u68c0\u51fa\u67d0\u6761\u6807\u8bb0\u7684\u6b63\u5411\u548c\u53cd\u5411\u8868\u793a\u65f6\uff0c\u53ea\u8bb0\u540c\u4e00\u4e2a\u7b49\u4f4d\uff0c\u4e0d\u56e0\u4e3a\u7ec4\u88c5\u65b9\u5411\u4e0d\u540c\u800c\u6f0f\u7b97\u6216\u91cd\u7b97\u3002<\/p>\n

\u4ece\u6bcf\u6761\u6a21\u677f\u5404\u53d6\u4e94\u767e\u6761\u65e0\u9519\u957f\u8bfb\u6bb5\uff0c\u6bcf\u6761\u957f\u5ea6\u4ecb\u4e8e\u516d\u5343\u516b\u767e\u548c\u4e5d\u5343\u516d\u767e\u4e4b\u95f4\uff0c\u4ea4\u66ff\u4f7f\u7528\u6b63\u5411\u548c\u53cd\u5411\u3002\u5c11\u91cf\u8bfb\u6bb5\u7279\u610f\u89e6\u53ca\u4e24\u7aef\uff0c\u5176\u4f59\u8d77\u70b9\u968f\u673a\u3002\u5c06\u4e24\u7ec4\u6df7\u5728\u4e00\u8d77\u4ea4\u7ed9\u7a0b\u5e8f\uff0c\u4e0d\u63d0\u4f9b\u4eb2\u672c\u5e8f\u5217\u3001\u67d3\u8272\u4f53\u6784\u8c61\u6570\u636e\u6216\u6807\u8bb0\u5217\u8868\u3002\u5b9e\u9a8c\u8bbe\u8ba1\u8005\u77e5\u9053\u4e24\u6761\u6a21\u677f\u662f\u8c01\uff0c\u7ec4\u88c5\u5668\u770b\u5230\u7684\u662f\u540c\u4e00\u4efd\u6df7\u5408\u957f\u8bfb\u6bb5\u3002\u9a8c\u6536\u65f6\u5206\u522b\u95ee\u67d0\u4e00\u6761\u7ec4\u88c5\u7247\u6bb5\u91cc\u6709\u6ca1\u6709\u53e6\u4e00\u6a21\u677f\u7684\u6807\u8bb0\uff0c\u4ee5\u53ca\u4e00\u6574\u4e2a\u5355\u500d\u578b\u6587\u4ef6\u662f\u5426\u5bb9\u7eb3\u4e86\u672c\u8be5\u5206\u5f00\u7684\u4e24\u79cd\u7247\u6bb5\u3002\u4e00\u4e2a\u7247\u6bb5\u5185\u6ca1\u6709\u6df7\u6742\uff0c\u5e76\u4e0d\u81ea\u52a8\u4fdd\u8bc1\u6574\u4e2a\u6587\u4ef6\u7684\u5206\u7ec4\u6b63\u786e\u3002<\/p>\n

\u540c\u65f6\u770b\u7247\u6bb5\u3001\u6587\u4ef6\u548c\u4e24\u5957\u6587\u4ef6\u7684\u5e76\u96c6<\/h2>\n

\u5b89\u88c5\u5e76\u8fd0\u884c hifiasm 0.25.0\uff0c\u5728\u4e3a\u5c0f\u57fa\u56e0\u7ec4\u5173\u95ed\u5e03\u9686\u8fc7\u6ee4\u5668\u7684\u540c\u4e00\u8bbe\u5b9a\u4e0b\uff0c\u5148\u8ba9\u7a0b\u5e8f\u81ea\u884c\u4f30\u8ba1\u8986\u76d6\u3002\u7b2c\u4e00\u4efd\u5355\u500d\u578b\u6587\u4ef6\u5f97\u5230\u4e24\u6761\u5404\u5341\u4e07\u78b1\u57fa\u7684\u7247\u6bb5\u3002\u7b2c\u4e00\u6761\u547d\u4e2d\u6a21\u677f\u7532\u7684\u4e09\u767e\u516b\u5341\u516b\u4e2a\u6807\u8bb0\uff0c\u6a21\u677f\u4e59\u7684\u6807\u8bb0\u4e3a\u96f6\u3002\u53e6\u4e00\u6761\u7684\u8ba1\u6570\u5012\u8fc7\u6765\u3002\u7b2c\u4e8c\u4efd\u5355\u500d\u578b\u6587\u4ef6\u4e5f\u5f97\u5230\u540c\u6837\u7684\u4e24\u6761\uff0c\u8fde\u4e3b\u7ec4\u88c5\u6587\u4ef6\u4e5f\u5982\u6b64\u3002\u6211\u4eec\u518d\u628a\u65b9\u5411\u7edf\u4e00\u6bd4\u8f83\uff0c\u4e24\u6761\u7247\u6bb5\u5206\u522b\u4e0e\u7532\u3001\u4e59\u5168\u957f\u9010\u78b1\u57fa\u5b8c\u5168\u76f8\u540c\u3002\u8fd9\u91cc\u786e\u5b9e\u4fdd\u4f4f\u4e86\u4e24\u79cd\u7b49\u4f4d\u7684\u5e8f\u5217\uff0c\u95ee\u9898\u5728\u4e8e\u6bcf\u4e2a\u5355\u500d\u578b\u6587\u4ef6\u90fd\u542b\u6709\u4e24\u5957\u5b8c\u6574\u5e8f\u5217\u3002<\/p>\n

\u82e5\u628a\u4e24\u4efd\u5355\u500d\u578b\u6587\u4ef6\u62fc\u6210\u4e00\u4e2a FASTA\uff0c\u603b\u957f\u5ea6\u4f1a\u662f\u56db\u5341\u4e07\uff0c\u800c\u6784\u9020\u7684\u4e8c\u500d\u4f53\u5408\u8ba1\u53ea\u6709\u4e8c\u5341\u4e07\u3002\u53ea\u770b\u201c\u4e24\u5957\u6807\u8bb0\u90fd\u627e\u9f50\u4e86\u201d\uff0c\u4e24\u8f6e\u90fd\u4f1a\u62a5\u6ee1\u5206\u3002\u53ea\u770b\u6bcf\u6761\u7247\u6bb5\u7684\u957f\u5ea6\u6216\u76f8\u4f3c\u5ea6\uff0c\u540c\u6837\u770b\u4e0d\u51fa\u91cd\u590d\u5206\u914d\u3002\u628a\u6587\u4ef6\u540d\u5f53\u4f5c\u4e00\u5217\uff0c\u7247\u6bb5\u540d\u5f53\u4f5c\u53e6\u4e00\u5217\uff0c\u518d\u5206\u522b\u7edf\u8ba1\u7532\u3001\u4e59\u6807\u8bb0\uff0c\u5c31\u80fd\u770b\u51fa\u91cd\u590d\u53d1\u751f\u5728\u54ea\u4e2a\u5c42\u9762\u3002\u5982\u679c\u662f\u771f\u5b9e\u57fa\u56e0\u6240\u5728\u533a\u57df\uff0c\u8fd8\u5e94\u67e5\u770b\u4e24\u6761\u5019\u9009\u7247\u6bb5\u4e0e\u4fa7\u7ffc\u662f\u5426\u4e00\u8d77\u5171\u7ebf\u3001\u662f\u5426\u5bf9\u9f50\u5230\u540c\u4e00\u4e2a\u7b49\u4f4d\u4f4d\u7f6e\u3002\u53ea\u51ed\u540c\u4e00\u4e2a\u57fa\u56e0\u540d\u51fa\u73b0\u4e24\u6b21\uff0c\u65e0\u6cd5\u5224\u65ad\u771f\u5b9e\u62f7\u8d1d\u6570\u3002hifiasm \u5404\u7c7b\u8f93\u51fa\u7684\u542b\u4e49<\/a><\/p>\n

\n\n\n\n\n\n\n
\u7528\u540c\u4e00\u4efd\u8bfb\u6bb5\u505a\u7ec4\u88c5<\/th>\n\u7b2c\u4e00\u5355\u500d\u578b\u6587\u4ef6<\/th>\n\u7b2c\u4e8c\u5355\u500d\u578b\u6587\u4ef6<\/th>\n\u4e24\u6587\u4ef6\u5e76\u96c6\u7684\u72ec\u7acb\u6807\u8bb0<\/th>\n<\/tr>\n<\/thead>\n
\u81ea\u52a8\u4f30\u8ba1\u8986\u76d6<\/td>\n\u7532 388\u3001\u4e59 388\uff0c\u4e24\u6761\u7247\u6bb5<\/td>\n\u7532 388\u3001\u4e59 388\uff0c\u4e24\u6761\u7247\u6bb5<\/td>\n\u7532 388\u3001\u4e59 388<\/td>\n<\/tr>\n
\u8bbe\u7f6e --hom-cov 82<\/code><\/td>\n\u7532 388\u3001\u4e59 0\uff0c\u4e00\u6761\u7247\u6bb5<\/td>\n\u7532 0\u3001\u4e59 388\uff0c\u4e00\u6761\u7247\u6bb5<\/td>\n\u7532 388\u3001\u4e59 388<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u62fc\u5bf9\u4e86\uff0c\u5374\u5206\u5230\u4e24\u8fb9\u3002\u4e24\u6761
\u4e24\u6761 100 kb \u6a21\u677f\u7684\u78b1\u57fa\u90fd\u627e\u56de\u4e86\uff0c\u8986\u76d6\u4f30\u8ba1\u6539\u53d8\u4e86\u7247\u6bb5\u5728\u54ea\u4e2a\u6587\u4ef6\u4e2d\u3002<\/figcaption><\/figure>\n

\u8ba1\u6570\u65f6\u8fd8\u8981\u9632\u6b62\u8f93\u5165\u6587\u4ef6\u672c\u8eab\u5236\u9020\u5047\u8c61\u3002\u56fe\u6587\u4ef6\u53ef\u80fd\u540c\u65f6\u6709\u5e26\u5e8f\u5217\u7684\u7248\u672c\u548c\u7701\u7565\u5e8f\u5217\u7684\u7248\u672c\uff0c\u540e\u8005\u7684\u7247\u6bb5\u884c\u4ee5\u661f\u53f7\u5360\u4f4d\u3002\u5e94\u53ea\u4ece\u542b\u5b9e\u9645\u5e8f\u5217\u7684\u7247\u6bb5\u884c\u5bfc\u51fa FASTA\uff0c\u8fde\u63a5\u884c\u53e6\u5b58\u4ee5\u4fbf\u8ffd\u67e5\u56fe\u7ed3\u6784\u3002\u6bcf\u6b21\u5bfc\u51fa\u540e\u6838\u5bf9\u7247\u6bb5\u6761\u6570\u3001\u603b\u957f\u5ea6\u548c\u552f\u4e00\u540d\u79f0\uff0c\u518d\u53bb\u7edf\u8ba1\u6807\u8bb0\uff0c\u53ef\u4ee5\u907f\u514d\u5c06\u540c\u4e00\u6279\u5e8f\u5217\u7684\u4e24\u79cd\u56fe\u6587\u4ef6\u4e00\u8d77\u52a0\u5165\u7ed3\u679c\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u5148\u4f30\u7b97\u8986\u76d6\u5cf0\u5e94\u8be5\u843d\u5728\u54ea\u91cc<\/h2>\n
hifiasm -f0 -t 2 -o auto reads.fa 2> auto.log\r\nhifiasm -f0 -t 2 --hom-cov 82 -o fixed reads.fa 2> fixed.log\r\nawk -F '\\t' '$1=="S"{print $2, length($3)}' fixed.bp.hap1.p_ctg.gfa\r\ngrep 'coverage threshold' auto.log fixed.log\r\n<\/code><\/pre>\n
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