{"id":66899,"date":"2026-11-14T19:32:35","date_gmt":"2026-11-14T11:32:35","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66899"},"modified":"2026-11-14T19:32:35","modified_gmt":"2026-11-14T11:32:35","slug":"hifiasm-hifi-haplotype-assembly-guide","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/hifiasm-hifi-haplotype-assembly-guide\/","title":{"rendered":"hifiasm \u4e3a\u4ec0\u4e48\u4f1a\u62fc\u51fa\u4e24\u5957\u5e8f\u5217\uff1f\u4ece HiFi \u8bfb\u6bb5\u5230\u5355\u500d\u578b\u7ec4\u88c5"},"content":{"rendered":"
\n

\u7b2c\u4e00\u6b21\u7528 hifiasm \u7ec4\u88c5\u4e8c\u500d\u4f53\u57fa\u56e0\u7ec4\uff0c\u7ed3\u679c\u76ee\u5f55\u91cc\u4f1a\u51fa\u73b0 hap1<\/code> \u548c hap2<\/code>\u3002\u5982\u679c\u4e00\u4e2a\u5019\u9009\u57fa\u56e0\u5728\u4e24\u4efd\u6587\u4ef6\u91cc\u5404\u6709\u4e00\u6761\u5e8f\u5217\uff0c\u80fd\u628a\u5b83\u4eec\u5206\u522b\u53eb\u4f5c\u7236\u672c\u548c\u6bcd\u672c\u62f7\u8d1d\u5417\uff1f\u5982\u679c\u4e24\u6761\u5e8f\u5217\u4e00\u6a21\u4e00\u6837\uff0c\u53c8\u662f\u7ec4\u88c5\u5931\u8d25\u4e86\u5417\uff1f<\/p>\n

\u8fd9\u4e24\u4e2a\u95ee\u9898\u90fd\u8981\u8ffd\u6eaf\u5230\u540c\u4e00\u4ef6\u4e8b\uff1a\u624b\u91cc\u7684\u8bfb\u6bb5\uff0c\u7a76\u7adf\u628a\u54ea\u4e9b\u5dee\u5f02\u8fde\u5728\u4e86\u540c\u4e00\u6761 DNA \u5206\u5b50\u4e0a\uff1f<\/strong> \u4e0b\u9762\u4ee5 hifiasm 0.25.0\u3001\u540c\u4e00\u4e2a\u4e8c\u500d\u4f53\u4e2a\u4f53\u7684 PacBio HiFi \u6570\u636e\u4e3a\u4f8b\uff0c\u6cbf\u7740\u8fd9\u6761\u8bc1\u636e\u8bfb\u61c2\u7ec4\u88c5\u7ed3\u679c\u3002hifiasm \u4ed3\u5e93\u4e0e\u7248\u672c<\/a><\/p>\n

\u4e00\u6761\u957f\u8bfb\u6bb5\uff0c\u600e\u6837\u5e2e\u52a9\u533a\u5206\u4e24\u5957\u5e8f\u5217\uff1f<\/h2>\n

\u5047\u8bbe\u67d0\u6bb5 DNA \u6709\u4e24\u4e2a\u6742\u5408\u4f4d\u70b9\u3002\u7b2c\u4e00\u4e2a\u4f4d\u7f6e\u6709 A \u548c G\uff0c\u7b2c\u4e8c\u4e2a\u6709 C \u548c T\u3002\u53ea\u77e5\u9053\u8fd9\u56db\u4e2a\u78b1\u57fa\uff0c\u8fd8\u65e0\u6cd5\u786e\u5b9a A \u4e0e C \u5728\u540c\u4e00\u6761\u67d3\u8272\u4f53\u4e0a\uff0c\u8fd8\u662f A \u4e0e T \u5728\u4e00\u8d77\u3002\u5982\u679c\u591a\u6761\u8de8\u8d8a\u4e24\u4e2a\u4f4d\u70b9\u7684 HiFi \u8bfb\u6bb5\u53cd\u590d\u8bfb\u5230 A\u2026C<\/strong>\uff0c\u53e6\u4e00\u6279\u53cd\u590d\u8bfb\u5230 G\u2026T<\/strong>\uff0c\u4e24\u5957\u5c40\u90e8\u7ec4\u5408\u5c31\u6709\u4e86\u76f4\u63a5\u7684\u5206\u5b50\u8bc1\u636e\u3002\u8fd9\u4e2a\u8fc7\u7a0b\u53eb\u5206\u76f8<\/strong>\u3002<\/p>\n

\"\u5206\u76f8\u793a\u610f\uff1a\u8de8\u8d8a\u4e24\u4e2a\u6742\u5408\u4f4d\u70b9\u7684\u8bfb\u6bb5\u652f\u6301<\/p>\n

HiFi \u7684\u957f\u5ea6\u8ba9\u4e00\u6761\u8bfb\u6bb5\u6709\u673a\u4f1a\u8de8\u8fc7\u591a\u4e2a\u5dee\u5f02\uff0c\u9ad8\u51c6\u786e\u5ea6\u5219\u6709\u52a9\u4e8e\u533a\u5206\u771f\u5b9e\u5dee\u5f02\u4e0e\u5076\u53d1\u6d4b\u5e8f\u9519\u8bef\u3002hifiasm \u5bfb\u627e\u8bfb\u6bb5\u4e4b\u95f4\u7684\u91cd\u53e0\uff0c\u5e76\u5728\u6821\u9519\u65f6\u53c2\u8003\u91cd\u53e0\u8bfb\u6bb5\u5728\u4fe1\u606f\u4f4d\u70b9\u662f\u5426\u4e00\u81f4\u3002\u8fd9\u6837\uff0c\u53e6\u4e00\u5957\u5355\u500d\u578b\u4e0a\u53cd\u590d\u51fa\u73b0\u7684\u771f\u5b9e\u78b1\u57fa\u5c31\u6709\u673a\u4f1a\u4fdd\u7559\u4e0b\u6765\u3002\u63a5\u7740\uff0c\u7a0b\u5e8f\u7528\u76f8\u5bb9\u7684\u91cd\u53e0\u5173\u7cfb\u5efa\u7acb\u7ec4\u88c5\u56fe\uff0c\u628a\u80fd\u8fde\u7eed\u5ef6\u4f38\u7684\u8def\u5f84\u62fc\u6210\u66f4\u957f\u7684\u5e8f\u5217\uff0c\u5373 contig\u3002\u8fd9\u4e2a\u8fc7\u7a0b\u53ef\u4ee5\u4ece\u8bfb\u6bb5\u51fa\u53d1\uff0c\u65e0\u9700\u5148\u6709\u53c2\u8003\u57fa\u56e0\u7ec4\u3002hifiasm \u539f\u59cb\u65b9\u6cd5\u8bba\u6587<\/a><\/p>\n

\u628a\u7ec4\u88c5\u56fe\u60f3\u6210\u6cbf\u5e8f\u5217\u5ef6\u4f38\u7684\u8def\u5f84\uff1a\u4e24\u5957\u62f7\u8d1d\u76f8\u540c\u7684\u90e8\u5206\u53ef\u4ee5\u5171\u7528\u4e00\u6bb5\u8def\u5f84\uff0c\u9047\u5230\u6742\u5408\u5dee\u5f02\u65f6\uff0c\u8def\u5f84\u53ef\u80fd\u5206\u5f00\uff0c\u968f\u540e\u518d\u6c47\u5408\u3002\u8fd9\u79cd\u5c40\u90e8\u7ed3\u6784\u5e38\u88ab\u79f0\u4e3a\u201c\u6c14\u6ce1\u201d\u3002\u8bfb\u56fe\u65f6\u8981\u7559\u610f\uff0c\u91cd\u590d\u5e8f\u5217\u548c\u6b8b\u4f59\u9519\u8bef\u4e5f\u53ef\u80fd\u9020\u6210\u5206\u652f\u3002\u770b\u5230\u6c14\u6ce1\uff0c\u8981\u56de\u5230\u8bfb\u6bb5\u652f\u6301\u548c\u90bb\u8fd1\u5e8f\u5217\uff0c\u624d\u80fd\u5224\u65ad\u5b83\u662f\u5426\u5bf9\u5e94\u4e00\u5bf9\u7b49\u4f4d\u5e8f\u5217\u3002<\/p>\n

\u54ea\u4e9b\u6570\u636e\u80fd\u628a\u5c40\u90e8\u5206\u76f8\u5ef6\u4f38\u5230\u66f4\u8fdc\uff1f<\/h2>\n

\u5047\u8bbe\u5de6\u8fb9\u4e00\u6bb5\u5df2\u7ecf\u5206\u6e05 A\/G\uff0c\u53f3\u8fb9\u4e00\u6bb5\u4e5f\u5206\u6e05 C\/T\uff0c\u4f46\u4e2d\u95f4\u662f\u4e00\u6bb5\u5f88\u957f\u7684\u7eaf\u5408\u5e8f\u5217\u3002\u82e5\u6ca1\u6709\u5355\u6761\u8bfb\u6bb5\u6216\u8fde\u7eed\u91cd\u53e0\u7684\u8bfb\u6bb5\u94fe\u628a\u4e24\u7aef\u7684\u4fe1\u606f\u4f4d\u70b9\u8fde\u8d77\u6765\uff0c\u5355\u9760\u5c40\u90e8\u5e8f\u5217\uff0c\u5c31\u53ef\u80fd\u65e0\u6cd5\u786e\u5b9a\u54ea\u4e00\u6761\u5de6\u4fa7\u8def\u5f84\u5e94\u8be5\u63a5\u4e0a\u54ea\u4e00\u6761\u53f3\u4fa7\u8def\u5f84\u3002\u201c\u4e24\u8fb9\u5404\u81ea\u5206\u5f97\u5f00\u201d\u548c\u201c\u4ece\u5de6\u5230\u53f3\u59cb\u7ec8\u5c5e\u4e8e\u540c\u4e00\u5957\u201d\u9700\u8981\u4e0d\u540c\u7684\u8bc1\u636e\u3002<\/strong><\/p>\n

\n\n\n\n\n\n\n\n
\u624b\u91cc\u6709\u4ec0\u4e48\u6570\u636e<\/th>\n\u989d\u5916\u4fe1\u606f\u4ece\u54ea\u91cc\u6765<\/th>\n\u62ff\u5230\u4e24\u5957\u8f93\u51fa\u540e\u600e\u6837\u89e3\u91ca<\/th>\n<\/tr>\n<\/thead>\n
\u53ea\u6709\u5b50\u4ee3 HiFi<\/td>\n\u540c\u4e00\u8bfb\u6bb5\u53ca\u76f8\u4e92\u91cd\u53e0\u7684\u8bfb\u6bb5\u628a\u6742\u5408\u4f4d\u70b9\u4e32\u6210\u5c40\u90e8\u533a\u5757\u3002\u8986\u76d6\u8db3\u591f\u3001\u4e24\u5957\u62f7\u8d1d\u90fd\u6709\u8bfb\u6bb5\u652f\u6301\uff0c\u4e14\u4fe1\u606f\u4f4d\u70b9\u80fd\u8fde\u7eed\u8854\u63a5\u65f6\uff0c\u5206\u76f8\u53ef\u4ee5\u5ef6\u4f38\u5f97\u66f4\u8fdc\u3002<\/td>\n\u9ed8\u8ba4\u8f93\u51fa\u4e3a\u90e8\u5206\u5206\u76f8\u7684\u4e24\u5957 contig\u3002\u8de8\u8fc7\u7f3a\u4e4f\u4fe1\u606f\u7684\u533a\u57df\uff0c\u4eb2\u672c\u5f52\u5c5e\u53ef\u80fd\u5207\u6362\uff1bhap1<\/code> \u7684\u7f16\u53f7\u672c\u8eab\u6ca1\u6709\u7236\u6e90\u542b\u4e49\u3002<\/td>\n<\/tr>\n
\u5b50\u4ee3 HiFi\uff0c\u52a0\u7236\u6bcd\u53cc\u65b9\u7684\u77ed\u8bfb\u6bb5<\/td>\n\u7528 yak \u5206\u522b\u7edf\u8ba1\u53cc\u4eb2\u7684\u77ed\u5e8f\u5217\u6807\u8bb0\uff08k-mer\uff09\uff0c\u501f\u52a9\u80fd\u533a\u5206\u53cc\u4eb2\u7684\u6807\u8bb0\u4e3a\u5b50\u4ee3\u7ec4\u88c5\u56fe\u4e0a\u7684\u8def\u5f84\u5b9a\u5411\u3002<\/td>\n\u82e5\u628a\u7236\u672c\u6807\u8bb0\u4ea4\u7ed9 -1<\/code>\u3001\u6bcd\u672c\u6807\u8bb0\u4ea4\u7ed9 -2<\/code>\uff0c\u4e24\u5957\u8f93\u51fa\u5c31\u6709\u76f8\u5e94\u7684\u4eb2\u672c\u89e3\u91ca\u3002\u4eb2\u672c\u6837\u672c\u8eab\u4efd\u3001\u6807\u8bb0\u8d28\u91cf\u53ca\u76ee\u6807\u533a\u57df\u6709\u6ca1\u6709\u6709\u6548\u6807\u8bb0\uff0c\u90fd\u5f71\u54cd\u8fd9\u4e00\u89e3\u91ca\u3002<\/td>\n<\/tr>\n
\u540c\u4e00\u4e2a\u4f53\u7684 HiFi \u548c Hi-C<\/td>\n\u6210\u5bf9\u7684 Hi-C \u8bfb\u6bb5\u63d0\u4f9b\u8fdc\u8ddd\u79bb\u63a5\u89e6\u4fe1\u606f\uff0c\u5e2e\u52a9\u5224\u65ad\u76f8\u9694\u8f83\u8fdc\u7684\u533a\u5757\u8be5\u5f52\u5230\u54ea\u4e00\u5957\u3002<\/td>\n\u53ef\u4ee5\u83b7\u5f97\u957f\u8ddd\u79bb\u5206\u76f8\u3002Hi-C \u672c\u8eab\u4e0d\u7ed9\u4e24\u5957\u5e8f\u5217\u51a0\u4ee5\u7236\u6e90\u6216\u6bcd\u6e90\uff0c\u5206\u76f8\u8de8\u5ea6\u4e5f\u5e94\u548c contig \u8fde\u7eed\u6027\u3001\u67d3\u8272\u4f53\u7ea7\u6302\u8f7d\u5206\u522b\u68c0\u67e5\u3002<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u540c\u4e00\u6bb5\u5728\u4e24\u5957\u7ed3\u679c\u91cc\u5b8c\u5168\u4e00\u81f4\uff0c\u53ef\u4ee5\u7b26\u5408\u771f\u5b9e\u7684\u7eaf\u5408\u72b6\u6001\u3002\u82e5\u957f\u91cd\u590d\u8d85\u8fc7\u4e86\u53ef\u6865\u63a5\u7684\u8303\u56f4\uff0c\u4e5f\u53ef\u80fd\u51fa\u73b0\u4e24\u4efd\u62f7\u8d1d\u88ab\u6298\u53e0\u7684\u60c5\u51b5\uff1b\u8fd9\u65f6\u8981\u67e5\u8986\u76d6\u3001\u62f7\u8d1d\u6570\u548c\u8de8\u8d8a\u91cd\u590d\u8fb9\u754c\u7684\u8bfb\u6bb5\u3002\u5355\u51ed\u201c\u76f8\u540c\u201d\u6216\u201c\u4e0d\u540c\u201d\u90fd\u5f88\u96be\u4e0b\u7ed3\u8bba\u3002\u4ee5\u4e0a\u8ba8\u8bba\u9762\u5411\u4e8c\u500d\u4f53\uff0c\u4e24\u5957\u8f93\u51fa\u4e0d\u80fd\u76f4\u63a5\u4ee3\u8868\u591a\u500d\u4f53\u7684\u5168\u90e8\u62f7\u8d1d\u3002\u4e09\u79cd\u6a21\u5f0f\u7684\u5b98\u65b9\u7528\u6cd5<\/a> \u00b7 Hi-C \u957f\u8ddd\u79bb\u5206\u76f8\u65b9\u6cd5<\/a><\/p>\n

\u5148\u8ba4\u6e05\u8f93\u51fa\u6587\u4ef6\uff0c\u518d\u5bfc\u51fa FASTA<\/h2>\n

\u4e0b\u9762\u662f\u53ea\u4f7f\u7528 HiFi \u7684\u547d\u4ee4\u793a\u4f8b\uff0c\u8f93\u5165\u6587\u4ef6\u540d\u548c\u7ebf\u7a0b\u6570\u6309\u5b9e\u9645\u73af\u5883\u66ff\u6362\u3002\u7b2c\u4e8c\u6761\u547d\u4ee4\u53ea\u5bfc\u51fa hap1\uff0c\u65b9\u4fbf\u8bf4\u660e GFA \u4e0e FASTA \u7684\u533a\u522b\u3002<\/p>\n

hifiasm -o sample.asm -t 16 reads.hifi.fastq.gz 2> sample.asm.log\r\nawk -F '\\t' '$1=="S" {print ">"$2; print $3}' sample.asm.bp.hap1.p_ctg.gfa > sample.hap1.fa\r\n<\/code><\/pre>\n
GFA \u4e2d\u7684 S<\/code> \u884c\u5b58\u653e\u5e8f\u5217\u7247\u6bb5\uff0cL<\/code> \u884c\u8bb0\u5f55\u7247\u6bb5\u95f4\u7684\u8fde\u63a5\u3002\u5bfc\u51fa\u7684 FASTA \u53ef\u4ee5\u7528\u4e8e\u6bd4\u5bf9\u548c\u6ce8\u91ca\uff1b\u539f\u59cb GFA \u8981\u7559\u4e0b\uff0c\u590d\u67e5\u65ad\u70b9\u6216\u5206\u652f\u65f6\u8fd8\u80fd\u770b\u5230\u56fe\u7ed3\u6784\u3002<\/p>\n
\n\n\n\n\n\n\n\n\n
\u5e38\u89c1\u6587\u4ef6\uff08\u7701\u7565 sample.asm<\/code> \u524d\u7f00\uff09<\/th>\n\u9002\u5408\u56de\u7b54\u7684\u95ee\u9898<\/th>\n<\/tr>\n<\/thead>\n
.bp.p_ctg.gfa<\/code><\/td>\n\u67e5\u770b\u4e3b\u7ec4\u88c5\u7684 contig\u3002\u4e3b\u7ec4\u88c5\u4ece\u4e0d\u540c\u533a\u6bb5\u9009\u62e9\u4ee3\u8868\u8def\u5f84\uff0c\u4e0d\u80fd\u76f4\u63a5\u5f53\u4f5c\u67d0\u4e00\u4e2a\u4eb2\u672c\u7684\u5b8c\u6574\u57fa\u56e0\u7ec4\u3002<\/td>\n<\/tr>\n
.bp.hap1.p_ctg.gfa<\/code>\u3001.bp.hap2.p_ctg.gfa<\/code><\/td>\n\u5bf9\u7167\u4ec5\u7528 HiFi \u5f97\u5230\u7684\u4e24\u5957\u90e8\u5206\u5206\u76f8\u7ed3\u679c\u3002\u60f3\u627e\u4e00\u4e2a\u57fa\u56e0\u7684\u4e24\u6761\u7b49\u4f4d\u5e8f\u5217\uff0c\u5e94\u4ece\u8fd9\u5bf9\u6587\u4ef6\u7684\u5bf9\u5e94\u533a\u57df\u5165\u624b\u3002<\/td>\n<\/tr>\n
.dip.hap1.p_ctg.gfa<\/code>\u3001.dip.hap2.p_ctg.gfa<\/code>\uff1bHi-C \u6a21\u5f0f\u5bf9\u5e94 .hic.hap1.p_ctg.gfa<\/code>\u3001.hic.hap2.p_ctg.gfa<\/code><\/td>\n\u6838\u5bf9\u6240\u9009\u5206\u76f8\u6a21\u5f0f\u7684\u8f93\u51fa\u3002\u6bd4\u8f83\u4e24\u5957\u7ec4\u88c5\u65f6\uff0c\u4fdd\u7559\u6a21\u5f0f\u3001\u8f93\u5165\u6837\u672c\u548c\u7248\u672c\u8bb0\u5f55\uff0c\u907f\u514d\u628a\u4e0d\u540c\u8fd0\u884c\u751f\u6210\u7684\u6587\u4ef6\u914d\u6210\u4e00\u5bf9\u3002<\/td>\n<\/tr>\n
*.bin<\/code>\u3001\u8fd0\u884c\u65e5\u5fd7<\/td>\n\u4e8c\u8fdb\u5236\u6587\u4ef6\u4fdd\u5b58\u6821\u6b63\u8bfb\u6bb5\u3001\u91cd\u53e0\u7b49\u4e2d\u95f4\u7ed3\u679c\uff0c\u517c\u5bb9\u7684\u540e\u7eed\u8fd0\u884c\u53ef\u4ee5\u590d\u7528\u3002\u65e5\u5fd7\u53ef\u7528\u4e8e\u786e\u8ba4\u8fd9\u4e00\u6b21\u5b9e\u9645\u8bfb\u5165\u4e86\u4ec0\u4e48\u3001\u662f\u5426\u590d\u7528\u4e86\u5df2\u6709\u7ed3\u679c\u3002<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u5b98\u65b9\u8f93\u51fa\u8bf4\u660e<\/a> \u00b7 0.25.0 \u547d\u4ee4\u4e0e\u7f13\u5b58\u8bf4\u660e<\/a><\/p>\n
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