{"id":71454,"date":"2026-11-15T00:55:11","date_gmt":"2026-11-14T16:55:11","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71454"},"modified":"2026-11-15T01:14:58","modified_gmt":"2026-11-14T17:14:58","slug":"haphic-refsort-scaffold-reverse-complement-agp-coordinate","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/haphic-refsort-scaffold-reverse-complement-agp-coordinate\/","title":{"rendered":"HapHiC \u5b9e\u8dd1\uff5c\u4e24\u6761 contig \u6b21\u5e8f\u548c\u6b63\u8d1f\u53f7\u90fd\u53d8\u4e86\uff0c\u600e\u6837\u5224\u65ad\u662f\u6574\u6761\u7ffb\u8f6c\u8fd8\u662f\u91cd\u65b0\u62fc\u63a5\uff1f"},"content":{"rendered":"
\n

\u6bd4\u8f83\u4e24\u7248\u67d3\u8272\u4f53\u7ec4\u88c5\u65f6\uff0c\u4f60\u53ef\u80fd\u770b\u5230\u7ec4\u4ef6\u4ece\u201c\u7532\u5728\u524d\u3001\u4e59\u5728\u540e\u201d\u53d8\u6210\u201c\u4e59\u5728\u524d\u3001\u7532\u5728\u540e\u201d\uff0c\u6bcf\u6761\u7ec4\u4ef6\u7684\u65b9\u5411\u4e5f\u90fd\u53cd\u4e86\u3002\u5355\u770b\u5750\u6807\u8868\uff0c\u8fd9\u5f88\u50cf\u526a\u5f00\u540e\u4ea4\u6362\u4e86\u4f4d\u7f6e\u3002\u53ef\u5982\u679c\u6574\u6761 scaffold \u53ea\u662f\u6539\u4e3a\u4ece\u53e6\u4e00\u7aef\u5f00\u59cb\u8bfb\uff0c\u5b83\u7684\u5185\u90e8\u63a5\u5934\u3001\u5e8f\u5217\u6210\u5458\u548c\u957f\u5ea6\u53ef\u4ee5\u5b8c\u5168\u76f8\u540c\u3002\u6211\u4eec\u8fd0\u884c HapHiC \u7684\u53c2\u8003\u6392\u5e8f\u547d\u4ee4\uff0c\u751f\u6210\u4e24\u5957\u771f\u5b9e\u7684\u5750\u6807\u8868\u53ca\u5e8f\u5217\uff0c\u9010\u78b1\u57fa\u533a\u522b\u4e24\u79cd\u89e3\u91ca\u3002\u672c\u7bc7\u4e13\u95e8\u9a8c\u8bc1\u4ea4\u4ed8\u524d\u7684\u53c2\u8003\u6392\u5e8f\u6b65\u9aa4\uff0c\u8f93\u5165\u5df2\u6709\u7ec4\u4ef6\u5e03\u5c40\u3002HapHiC \u5b98\u65b9\u9879\u76ee<\/a><\/p>\n

\u54ea\u4e9b\u6587\u4ef6\u51b3\u5b9a\u4e86\u4e00\u4efd\u6392\u5e8f\u7ed3\u679c<\/h2>\n

\u539f\u59cb FASTA \u4fdd\u5b58 contig \u7684\u78b1\u57fa\u3002AGP \u6587\u4ef6\u9010\u6bb5\u63cf\u8ff0\u6bcf\u6761 scaffold \u7531\u54ea\u4e9b\u7ec4\u4ef6\u7ec4\u6210\u3001\u653e\u7f6e\u65b9\u5411\u5982\u4f55\u3001\u95f4\u9694\u7559\u591a\u5c11\u672a\u77e5\u78b1\u57fa\u3002\u7b2c\u4e09\u4efd\u8f93\u5165\u662f\u539f\u59cb\u7ec4\u4ef6\u4e0e\u53c2\u8003\u67d3\u8272\u4f53\u7684\u6bd4\u5bf9\uff0c\u5bf9\u5e94\u54ea\u4e2a\u67d3\u8272\u4f53\u3001\u5728\u54ea\u4e2a\u65b9\u5411\u3001\u8986\u76d6\u591a\u957f\uff0c\u90fd\u4ece\u8fd9\u91cc\u6765\u3002\u5173\u952e\u662f\u4f7f\u7528\u548c AGP \u7ec4\u4ef6\u680f\u4e00\u81f4\u7684\u5e8f\u5217\u540d\u3002\u82e5\u628a\u6210\u54c1 scaffold \u5f53\u4f5c\u67e5\u8be2\u5e8f\u5217\u53bb\u6bd4\u5bf9\uff0c\u518d\u628a\u7ed3\u679c\u4ea4\u7ed9\u671f\u5f85\u539f\u59cb contig \u540d\u7684\u6b65\u9aa4\uff0c\u6587\u4ef6\u770b\u4e0a\u53bb\u90fd\u6709\u78b1\u57fa\u548c\u5750\u6807\uff0c\u5374\u6ca1\u6cd5\u628a\u8bc1\u636e\u6b63\u786e\u5173\u8054\u5230\u6307\u5b9a\u7ec4\u4ef6\u3002\u4f5c\u8005\u7684\u53c2\u8003\u6392\u5e8f\u548c\u8f93\u5165\u8bf4\u660e<\/a><\/p>\n

\u8bfb\u8fd9\u7c7b\u6570\u636e\u5148\u9009\u4e00\u4e2a\u6709\u65b9\u5411\u7684\u63a5\u5934\u3002\u539f\u5e03\u5c40\u82e5\u662f\u6b63\u5411\u7684\u7532\uff0c\u63a5\u4e00\u767e\u4e2a\u672a\u77e5\u78b1\u57fa\uff0c\u518d\u63a5\u6b63\u5411\u7684\u4e59\uff0c\u90a3\u4e48\u4ece\u53e6\u4e00\u7aef\u8bfb\uff0c\u987a\u5e8f\u5fc5\u7136\u53d8\u6210\u53cd\u5411\u4e92\u8865\u7684\u4e59\u3001\u540c\u6837\u7684\u4e00\u767e\u4e2a\u672a\u77e5\u78b1\u57fa\u3001\u53cd\u5411\u4e92\u8865\u7684\u7532\u3002\u6574\u6761\u7ffb\u8f6c\u4f1a\u540c\u65f6\u6539\u53d8\u7ec4\u4ef6\u6b21\u5e8f\u548c\u65b9\u5411\u3002\u5982\u679c\u4e24\u7248\u4ea4\u6362\u4e86\u7ec4\u4ef6\u7684\u6b21\u5e8f\u5374\u53ea\u7ffb\u8f6c\u5176\u4e2d\u4e00\u6761\uff0c\u6216\u628a\u4e2d\u95f4\u7684\u63a5\u5934\u6362\u5230\u522b\u5904\uff0c\u7b80\u5355\u7684\u6574\u6761\u7ffb\u8f6c\u4fbf\u89e3\u91ca\u4e0d\u4e86\u3002\u8fd9\u6761\u5224\u65ad\u53ea\u7528\u5230\u5e8f\u5217\u672c\u8eab\uff0c\u9002\u5408\u5728\u770b\u70ed\u56fe\u6216\u5171\u7ebf\u56fe\u524d\u5148\u505a\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4e94\u4e2a\u539f\u59cb\u7ec4\u4ef6\uff0c\u4e24\u6761\u53c2\u8003\u67d3\u8272\u4f53<\/h2>\n

\u6211\u4eec\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\u6784\u9020\u4e94\u6761\u552f\u4e00\u5e8f\u5217\u3002\u7532\u7ec4\u7531\u4e24\u4e07\u548c\u4e00\u4e07\u4e03\u5343\u78b1\u57fa\u7684\u4e24\u4e2a\u7ec4\u4ef6\u7ec4\u6210\uff0c\u4e59\u7ec4\u7531\u4e24\u4e07\u4e8c\u5343\u548c\u4e00\u4e07\u516b\u5343\u78b1\u57fa\u7684\u4e24\u4e2a\u7ec4\u4ef6\u7ec4\u6210\uff0c\u53e6\u6709\u56db\u5343\u4e94\u767e\u78b1\u57fa\u7684\u4e00\u6761\u5355\u72ec\u653e\u7f6e\u3002\u4e24\u4e2a\u5df2\u62fc\u63a5\u7ec4\u5404\u7559\u4e00\u767e\u4e2a\u672a\u77e5\u78b1\u57fa\u3002\u5236\u4f5c\u6a21\u62df\u53c2\u8003\u65f6\uff0c\u628a\u7532\u7ec4\u6574\u4f53\u53cd\u5411\u4e92\u8865\uff0c\u4e59\u7ec4\u4fdd\u6301\u539f\u65b9\u5411\uff0c\u5355\u72ec\u7ec4\u4ef6\u4e0d\u653e\u8fdb\u53c2\u8003\u3002\u7528 minimap2 \u4e3a\u539f\u59cb contig \u5b9e\u9645\u751f\u6210\u6bd4\u5bf9\u8868\uff0c\u56db\u4e2a\u53ef\u5339\u914d\u7ec4\u4ef6\u90fd\u7aef\u5230\u7aef\u6620\u5c04\uff0c\u6620\u5c04\u8d28\u91cf\u5747\u4e3a\u516d\u5341\u3002\u7136\u540e\u5b89\u88c5 HapHiC 1.0.7 \u7684\u4f9d\u8d56\uff0c\u8fd0\u884c\u4e24\u6b21 refsort<\/code>\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u6761\u4ef6<\/th>\n\u8f93\u51fa\u7684 scaffold \u987a\u5e8f<\/th>\n\u7532\u7ec4\u7684\u7ec4\u4ef6\u548c\u65b9\u5411<\/th>\n\u4e59\u7ec4\u548c\u5355\u72ec\u7ec4\u4ef6<\/th>\n<\/tr>\n<\/thead>\n
\u539f\u59cb\u5e03\u5c40<\/td>\nscB\u3001scA\u3001unplaced<\/td>\na \u6b63\u5411\u3001b \u6b63\u5411<\/td>\nc \u4e0e d \u6b63\u5411\uff0ce \u5355\u72ec<\/td>\n<\/tr>\n
\u6309\u53c2\u8003\u9ed8\u8ba4\u987a\u5e8f\u8f93\u51fa<\/td>\nscA\u3001scB\u3001unplaced<\/td>\nb \u53cd\u5411\u3001a \u53cd\u5411<\/td>\n\u4e0e\u539f\u59cb\u76f8\u540c<\/td>\n<\/tr>\n
\u6307\u5b9a\u5148\u5217 chrB \u518d\u5217 chrA<\/td>\nscB\u3001scA\u3001unplaced<\/td>\nb \u53cd\u5411\u3001a \u53cd\u5411<\/td>\n\u4e0e\u539f\u59cb\u76f8\u540c<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u628a\u8f93\u51fa\u7684\u7532\u7ec4\u9010\u78b1\u57fa\u4e0e\u539f\u59cb\u7532\u7ec4\u7684\u53cd\u5411\u4e92\u8865\u6bd4\u8f83\uff0c\u4e09\u4e07\u4e03\u5343\u4e00\u767e\u4e2a\u4f4d\u7f6e\u5168\u90e8\u4e00\u81f4\uff0c\u4e2d\u95f4\u4ecd\u662f\u4e00\u767e\u4e2a\u672a\u77e5\u78b1\u57fa\u3002\u4e59\u7ec4\u56db\u4e07\u96f6\u4e00\u767e\u4e2a\u78b1\u57fa\u9010\u5b57\u76f8\u540c\uff0c\u672a\u653e\u7f6e\u7ec4\u4ef6\u4e5f\u5b8c\u6574\u4fdd\u7559\u3002\u4e24\u6b21\u6392\u5e8f\u7684\u6587\u4ef6\u987a\u5e8f\u4e0d\u540c\uff0c\u4f46\u6309 scaffold \u540d\u5206\u522b\u8ba1\u7b97\u5e8f\u5217\u6821\u9a8c\u503c\uff0c\u4e09\u4e2a\u6761\u76ee\u5728\u4e24\u6b21\u8f93\u51fa\u95f4\u4e00\u4e00\u76f8\u540c\u3002\u8fd9\u4e24\u6b21\u8fd0\u884c\u65e2\u6ca1\u6709\u5f15\u5165\u65b0\u63a5\u5934\uff0c\u4e5f\u6ca1\u6709\u628a\u672a\u653e\u7f6e\u7ec4\u4ef6\u951a\u5230\u53c2\u8003\u4e0a\u3002\u53ef\u4ee5\u4ece\u9010\u6761\u78b1\u57fa\u3001\u7ec4\u4ef6\u8eab\u4efd\u548c\u771f\u5b9e\u8f93\u51fa\u540c\u65f6\u590d\u6838\u3002 <\/p>\n

\"\u4e24\u4e2a\u7ec4\u4ef6\u90fd\u7ffb\u8f6c\uff0c\u63a5\u5934\u8fd8\u5728\u5417\u3002\u7528\u771f\u5b9e\u6bd4\u5bf9\u548c
\u7528\u771f\u5b9e\u6bd4\u5bf9\u548c AGP \u9010\u78b1\u57fa\u6838\u5bf9\u4e00\u6761 37100 bp \u7684 scaffold\u3002<\/figcaption><\/figure>\n

\u6574\u6761\u7ffb\u8f6c\u540e\uff0c\u65e7\u6ce8\u91ca\u5750\u6807\u600e\u6837\u6362\u7b97<\/h2>\n

\u5bf9\u8fd9\u6837\u4e00\u6761\u4ec5\u6574\u4f53\u7ffb\u8f6c\u3001\u4e14\u957f\u5ea6\u5df2\u6838\u5b9e\u4e3a\u4e09\u4e07\u4e03\u5343\u4e00\u767e\u7684\u5e8f\u5217\uff0c\u53ef\u4ee5\u9009\u4e00\u4e2a\u5c0f\u533a\u95f4\u624b\u7b97\u3002\u539f\u6765\u4e00\u5f00\u59cb\u8ba1\u6570\u5e76\u5305\u542b\u4e24\u7aef\u7684\u7b2c\u4e00\u767e\u96f6\u4e00\u5230\u7b2c\u4e8c\u767e\u4f4d\uff0c\u7ffb\u8f6c\u540e\u843d\u5728\u7b2c\u4e09\u4e07\u516d\u5343\u4e5d\u767e\u96f6\u4e00\u5230\u7b2c\u4e09\u4e07\u4e03\u5343\u4f4d\uff0c\u540c\u65f6\u8981\u4ea4\u6362\u94fe\u65b9\u5411\u3002\u8ba1\u7b97\u8fc7\u7a0b\u662f\u7528\u603b\u957f\u5ea6\u51cf\u53bb\u539f\u6765\u7684\u53f3\u7aef\u518d\u52a0\u4e00\uff0c\u5f97\u5230\u65b0\u7684\u5de6\u7aef\uff0c\u518d\u7528\u603b\u957f\u5ea6\u51cf\u539f\u6765\u7684\u5de6\u7aef\u52a0\u4e00\u4f5c\u4e3a\u53f3\u7aef\u3002\u82e5\u91c7\u7528\u4ece\u96f6\u5f00\u59cb\u7684\u534a\u5f00\u533a\u95f4\uff0c\u516c\u5f0f\u7684\u52a0\u4e00\u5e94\u76f8\u5e94\u6539\u53d8\u3002\u5b9e\u9645\u8f6c\u6362\u524d\u5148\u628a\u539f\u533a\u95f4\u63d0\u53d6\u51fa\u6765\uff0c\u5bf9\u65b0\u4f4d\u7f6e\u62ff\u5230\u7684\u5e8f\u5217\u505a\u53cd\u5411\u4e92\u8865\uff0c\u4e24\u7aef\u548c\u65b9\u5411\u90fd\u80fd\u9010\u5b57\u6838\u5bf9\u3002<\/p>\n

minimap2 -x asm5 -c --secondary=no ref.fa contigs.fa > ref.paf\r\nhaphic refsort raw.agp ref.paf --fasta contigs.fa \\\r\n  --fout default.fa > default.agp\r\nhaphic refsort raw.agp ref.paf --fasta contigs.fa --ref_order chrB,chrA \\\r\n  --fout reordered.fa > reordered.agp\r\n<\/code><\/pre>\n
\u5982\u679c\u53ea\u6709\u591a\u6761 scaffold \u5728 FASTA \u91cc\u7684\u6392\u5217\u987a\u5e8f\u53d8\u4e86\uff0c\u5f88\u591a\u5e8f\u5217\u7d22\u5f15\u5de5\u5177\u4ecd\u6839\u636e\u540d\u79f0\u627e\u6570\u636e\uff0c\u4f46\u65e7\u7d22\u5f15\u91cc\u7684\u6587\u4ef6\u504f\u79fb\u91cf\u53ef\u80fd\u5df2\u5931\u6548\u3002\u91cd\u65b0\u751f\u6210\u4e0e\u65b0\u6587\u4ef6\u5bf9\u5e94\u7684\u7d22\u5f15\uff0c\u518d\u6838\u5bf9\u67d3\u8272\u4f53\u540d\u3001\u957f\u5ea6\u548c\u65b9\u5411\u3002\u82e5\u6807\u6ce8\u4f9d\u9644\u4e8e\u7ffb\u8f6c\u7684\u7532\u7ec4\uff0c\u91c7\u7528\u76f8\u540c\u540d\u5b57\u5e76\u4e0d\u4f1a\u81ea\u52a8\u4fee\u6b63\u539f\u6765\u7684\u57fa\u56e0\u5750\u6807\u3002\u540c\u7406\uff0c\u53d8\u5f02\u4f4d\u7f6e\u548c\u53c2\u8003\u7b49\u4f4d\u5e8f\u5217\u4e5f\u8981\u5bf9\u65b0\u53c2\u8003\u9010\u9879\u6838\u5b9e\u3002\u4e3a\u4e86\u8ffd\u6eaf\uff0c\u53ef\u4ee5\u4fdd\u7559\u65e7\u65b0\u4e24\u7248\u5e03\u5c40\u3001\u539f\u59cb\u7ec4\u4ef6\u6587\u4ef6\u548c\u4f4d\u70b9\u8f6c\u6362\u8868\uff0c\u907f\u514d\u4ec5\u4ea4\u4ed8\u540c\u540d\u5e8f\u5217\u8ba9\u4e0b\u6e38\u8bef\u4ee5\u4e3a\u5750\u6807\u53ef\u76f4\u63a5\u6cbf\u7528\u3002<\/p>\n
\u6536\u5230\u4e24\u4e2a\u7248\u672c\u65f6\uff0c\u6211\u4f1a\u5148\u6309 scaffold \u540d\u6bd4\u8f83\u957f\u5ea6\u3001\u672a\u77e5\u78b1\u57fa\u6570\u548c\u539f\u5411\u5e8f\u5217\u6821\u9a8c\u503c\uff0c\u53ea\u6709\u539f\u5411\u6838\u5bf9\u4e0d\u4e00\u81f4\u7684\u624d\u7ee7\u7eed\u67e5\u53cd\u5411\u4e92\u8865\u3002\u5982\u679c\u6362\u5411\u540e\u4ecd\u7136\u4e0d\u4e00\u81f4\uff0c\u518d\u6cbf\u7ec4\u4ef6\u8868\u9010\u4e00\u6bd4\u8f83\u6210\u5458\u3001\u7ec4\u4ef6\u91c7\u7528\u7684\u8d77\u6b62\u5750\u6807\u3001\u95f4\u9694\u957f\u5ea6\u548c\u63a5\u5934\u3002\u4e24\u4e2a\u540c\u540d\u7ec4\u4ef6\u82e5\u4f7f\u7528\u4e86\u4e0d\u540c\u7684\u622a\u53d6\u8303\u56f4\uff0c\u5373\u4f7f\u56fe\u4e0a\u987a\u5e8f\u548c\u6b63\u8d1f\u53f7\u90fd\u4e00\u81f4\uff0c\u4e5f\u5df2\u7ecf\u6539\u53d8\u4e86\u4ea4\u4ed8\u5e8f\u5217\u3002\u628a\u6838\u67e5\u4e00\u6b65\u6b65\u6536\u7a84\u5230\u5177\u4f53\u7ec4\u4ef6\uff0c\u80fd\u76f4\u63a5\u6307\u51fa\u5e94\u8be5\u8bf7\u54ea\u4e00\u65b9\u56de\u5230\u4e0a\u6e38\u6587\u4ef6\u6838\u5b9e\u3002<\/p>\n
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