{"id":71505,"date":"2026-11-15T01:10:52","date_gmt":"2026-11-14T17:10:52","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71505"},"modified":"2026-11-15T01:15:11","modified_gmt":"2026-11-14T17:15:11","slug":"pggb-partition-alignment-length-weight-community-contigs","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/pggb-partition-alignment-length-weight-community-contigs\/","title":{"rendered":"PGGB \u5b9e\u8dd1\uff5c\u516d\u6761 contig \u7684\u76f8\u4f3c\u6027\u7f51\u7edc\uff0c\u53ea\u6539\u4e00\u6761\u6bd4\u5bf9\uff0c\u4e3a\u4ec0\u4e48\u5206\u533a\u4ece\u4e24\u4e2a\u53d8\u6210\u4e09\u4e2a\uff1f"},"content":{"rendered":"<div class=\"ysx-method-guide\" style=\"max-width:820px;min-width:0;margin:0 auto;color:#26374a;line-height:1.86;overflow-wrap:anywhere\">\n<p>\u628a\u591a\u4e2a\u4e2a\u4f53\u7684\u67d3\u8272\u4f53\u4e00\u8d77\u5efa\u6cdb\u57fa\u56e0\u7ec4\u56fe\u524d\uff0c\u5e38\u4f1a\u5148\u6309\u5e8f\u5217\u76f8\u4f3c\u6027\u5206\u533a\uff0c\u5e0c\u671b\u628a\u5bf9\u5e94\u7684\u67d3\u8272\u4f53\u653e\u5728\u4e00\u8d77\u3002\u4e00\u4e2a\u770b\u4f3c\u7b80\u5355\u7684\u95ee\u9898\u662f\uff0c\u4e24\u4e2a\u5e8f\u5217\u6807\u8bc6\u91cc\u90fd\u5199\u7740\u540c\u4e00\u67d3\u8272\u4f53\u540d\uff0c\u5b83\u4eec\u5c31\u4e00\u5b9a\u5206\u5230\u540c\u4e00\u4e2a\u793e\u533a\u5417\uff1f\u6211\u4eec\u5b9e\u9645\u8fd0\u884c PGGB 0.7.4 \u53d1\u884c\u7248\u7684\u4e24\u4e2a\u5206\u533a\u811a\u672c\uff0c\u4fdd\u6301\u5e8f\u5217\u540d\u79f0\u548c\u6bd4\u5bf9\u603b\u884c\u6570\u4e0d\u53d8\uff0c\u53ea\u6539\u4e00\u6761\u8de8\u7ec4\u6bd4\u5bf9\u7684\u957f\u5ea6\u3002\u7ed3\u679c\u4ece\u4e24\u4e2a\u793e\u533a\u53d8\u6210\u4e09\u4e2a\uff0c\u540c\u4e00\u6837\u672c\u7684\u4e24\u6761\u4e0d\u540c\u67d3\u8272\u4f53\u53cd\u800c\u88ab\u5355\u72ec\u5206\u5728\u4e00\u8d77\u3002<a style=\"color:#905321;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/github.com\/pangenome\/pggb\">PGGB \u5b98\u65b9\u9879\u76ee<\/a><\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u5148\u770b\u7f51\u7edc\u4e2d\u7684\u4e00\u6761\u8fb9\u662f\u4ec0\u4e48<\/h2>\n<p>PGGB \u7684 <code>partition-before-pggb<\/code> \u6d41\u7a0b\u53ef\u4ee5\u628a\u57fa\u56e0\u7ec4\u5e8f\u5217\u95f4\u7684\u6bd4\u5bf9\u8f6c\u6210\u5e26\u6743\u7f51\u7edc\uff0c\u518d\u6839\u636e\u7f51\u7edc\u793e\u533a\u62c6\u5206\u5efa\u56fe\u8f93\u5165\u3002\u5728\u672c\u6b21\u9a8c\u8bc1\u7684\u4e24\u4e2a\u811a\u672c\u4e2d\uff0c\u9876\u70b9\u662f\u51fa\u73b0\u5728\u6bd4\u5bf9\u91cc\u7684\u5e8f\u5217\u540d\uff0c\u4e00\u6761\u8f93\u5165\u6bd4\u5bf9\u8d21\u732e\u4e00\u6761\u5e26\u6743\u7684\u8fb9\u3002\u4f5c\u8005\u7684\u8f6c\u6362\u811a\u672c\u4f7f\u7528\u6bd4\u5bf9\u957f\u5ea6\u4e58\u4ee5\u767e\u5206\u5236\u4e00\u81f4\u6027\u518d\u9664\u4ee5\u4e00\u767e\u3002\u4e24\u6bb5\u53ea\u6709\u4e00\u5c0f\u622a\u9ad8\u5ea6\u76f8\u540c\uff0c\u548c\u4e24\u6761\u5e8f\u5217\u957f\u8ddd\u79bb\u4fdd\u6301\u9ad8\u5ea6\u76f8\u540c\uff0c\u5355\u770b\u767e\u5206\u6bd4\u53ef\u80fd\u5dee\u4e0d\u591a\uff0c\u5f62\u6210\u7684\u8fb9\u6743\u5374\u5dee\u5f88\u591a\u3002<a style=\"color:#905321;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/github.com\/pangenome\/pggb\/blob\/v0.7.4\/scripts\/paf2net.py\">PGGB \u8fb9\u6743\u8f6c\u6362\u6e90\u7801<\/a><\/p>\n<p>\u793e\u533a\u68c0\u6d4b\u4f7f\u7528\u7684\u662f\u8fd9\u6837\u7684\u8fb9\u548c\u6743\u91cd\u3002\u7b97\u6cd5\u5e76\u4e0d\u4f1a\u56e0\u4e3a\u5e8f\u5217\u540d\u5199\u7740\u7b2c\u4e00\u6761\u6216\u7b2c\u4e8c\u6761\u67d3\u8272\u4f53\uff0c\u5c31\u5f3a\u5236\u5b83\u7559\u5728\u67d0\u4e2a\u7ec4\u91cc\u3002\u89c4\u8303\u7684\u6837\u672c\u4e0e\u67d3\u8272\u4f53\u547d\u540d\u5bf9\u4eba\u5224\u65ad\u5f52\u5c5e\u3001\u8ffd\u8e2a\u5f02\u5e38\u5f88\u91cd\u8981\uff0c\u4f46\u4e0d\u80fd\u4ee3\u66ff\u6bd4\u5bf9\u8bc1\u636e\u3002\u5982\u679c\u4e00\u6bb5\u5f88\u957f\u7684\u5e8f\u5217\u540c\u65f6\u51fa\u73b0\u5728\u4e24\u4e2a\u5e76\u975e\u540c\u6e90\u7684\u67d3\u8272\u4f53\u6807\u7b7e\u4e0b\uff0c\u4f8b\u5982\u5927\u578b\u8fd1\u4f3c\u91cd\u590d\u3001\u6613\u4f4d\u7247\u6bb5\u6216\u4e00\u6761\u9519\u62fc\u7684 contig\uff0c\u5206\u533a\u9996\u5148\u770b\u5230\u7684\u662f\u5f88\u5f3a\u7684\u8fde\u63a5\u3002\u5b83\u4e0d\u80fd\u4ec5\u6839\u636e\u8fde\u63a5\u81ea\u884c\u5224\u65ad\u80cc\u540e\u7684\u751f\u7269\u5b66\u539f\u56e0\u3002<a style=\"color:#905321;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/github.com\/pangenome\/pggb\/blob\/v0.7.4\/scripts\/net2communities.py\">PGGB \u793e\u533a\u68c0\u6d4b\u6e90\u7801<\/a><\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4fdd\u6301\u4e03\u6761\u8fb9\uff0c\u53ea\u6539\u53d8\u7b2c\u4e03\u6761\u7684\u957f\u5ea6<\/h2>\n<p>\u6211\u4eec\u58f0\u660e\u4e09\u4e2a\u6837\u672c\uff0c\u6bcf\u4e2a\u6837\u672c\u5404\u6709\u4e24\u6761\u4e09\u4e07\u78b1\u57fa\u7684\u793a\u4f8b\u67d3\u8272\u4f53\uff0c\u53e6\u5217\u4e00\u6761\u6ca1\u6709\u4efb\u4f55\u5339\u914d\u8bb0\u5f55\u7684\u989d\u5916\u7ec4\u4ef6\u3002\u8fd9\u91cc\u7684\u8f93\u5165\u662f\u6784\u9020\u7684\u6bd4\u5bf9\u8868\uff0c\u6ca1\u6709\u4eba\u4e3a\u5236\u9020\u4e00\u6574\u5957\u6d4b\u5e8f\u6216\u7ec4\u88c5\u78b1\u57fa\u3002\u5bf9\u540c\u4e00\u67d3\u8272\u4f53\u7684\u4e09\u4e2a\u6837\u672c\u4e24\u4e24\u8fde\u7ebf\uff0c\u6bcf\u7ec4\u4e09\u6761\uff0c\u5408\u8ba1\u516d\u6761\u3002\u6bcf\u6761\u7ec4\u5185\u6bd4\u5bf9\u5747\u957f\u4e00\u4e07\u78b1\u57fa\uff0c\u4e00\u81f4\u6027\u4e3a\u767e\u5206\u4e4b\u4e5d\u5341\u516b\uff0c\u5f97\u5230\u7684\u8fb9\u6743\u5404\u4e3a\u4e5d\u5343\u516b\u767e\u3002\u7b2c\u4e03\u6761\u8fb9\u628a\u6837\u672c C \u7684\u4e24\u6761\u4e0d\u540c\u67d3\u8272\u4f53\u76f8\u8fde\uff0c\u4e00\u81f4\u6027\u56fa\u5b9a\u5728\u767e\u5206\u4e4b\u4e5d\u5341\u4e5d\uff0c\u53ea\u6539\u53d8\u6bd4\u5bf9\u957f\u5ea6\u3002<\/p>\n<div class=\"guide-table\" style=\"max-width:100%;overflow-x:auto;margin:18px 0\">\n<table style=\"display:table;width:100%;max-width:100%;min-width:0;table-layout:fixed;border-collapse:collapse;font-size:.92em;line-height:1.6\">\n<thead>\n<tr>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#fff3e7;color:#1e293b;vertical-align:top;text-align:left;padding:6px;border:1px solid #c4cfdb\">\u7b2c\u4e03\u6761\u8fb9<\/th>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#fff3e7;color:#1e293b;vertical-align:top;text-align:right;padding:6px;border:1px solid #c4cfdb\">\u8f6c\u6362\u540e\u6743\u91cd<\/th>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#fff3e7;color:#1e293b;vertical-align:top;text-align:left;padding:6px;border:1px solid #c4cfdb\">\u516d\u6b21\u5206\u533a\u7684\u6210\u5458\u7ed3\u679c<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u957f 1000 bp<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">990<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u4e24\u7ec4\u5404\u4e09\u6761\uff0c\u5206\u522b\u542b A\u3001B\u3001C \u7684\u540c\u53f7\u67d3\u8272\u4f53<\/td>\n<\/tr>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u957f 28000 bp<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">27720<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u4e09\u7ec4\u5404\u4e24\u6761\uff0cA \u4e0e B \u4ecd\u6309\u67d3\u8272\u4f53\u53f7\u914d\u5bf9\uff0cC \u7684\u4e24\u6761\u67d3\u8272\u4f53\u81ea\u6210\u4e00\u7ec4<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<p>\u4e24\u79cd\u8f93\u5165\u90fd\u5b9e\u9645\u8fd0\u884c\u4e86\u6743\u91cd\u8f6c\u6362\uff0c\u5e76\u5404\u8fd0\u884c\u516d\u6b21\u4f5c\u8005\u7684\u793e\u533a\u68c0\u6d4b\u811a\u672c\uff0c\u4f7f\u7528\u5728\u5b9e\u9a8c\u73af\u5883\u4e2d\u8bb0\u5f55\u7684 igraph 1.0.0\u3002\u6bd4\u8f83\u91cd\u590d\u8fd0\u884c\u65f6\uff0c\u6211\u4eec\u628a\u6210\u5458\u540d\u6392\u5e8f\u518d\u6bd4\u8f83\uff0c\u5ffd\u7565\u793e\u533a\u7f16\u53f7\uff0c\u540c\u4e00\u6761\u4ef6\u7684\u516d\u6b21\u6210\u5458\u5212\u5206\u4e00\u81f4\u3002\u5f3a\u8fde\u63a5\u628a C \u7684\u4e24\u6761\u67d3\u8272\u4f53\u62c9\u8fdb\u4e00\u4e2a\u72ec\u7acb\u7684\u5c0f\u7ec4\uff0c\u5176\u4f59\u5404\u6709\u4e24\u6761\u7684\u4e24\u7ec4\u4ecd\u4fdd\u7559\u4e0b\u6765\u3002\u4e8e\u662f\u589e\u52a0\u4e00\u4e2a\u8de8\u7ec4\u8fb9\u7684\u6743\u91cd\uff0c\u5e26\u6765\u7684\u7ed3\u679c\u662f\u591a\u51fa\u4e00\u4e2a\u793e\u533a\u3002\u8fd9\u6b21\u53ea\u9a8c\u8bc1\u5de5\u5177\u91cc\u7684\u5206\u533a\u9636\u6bb5\uff0c\u6ca1\u6709\u8fd0\u884c\u540e\u7eed\u5168\u5e8f\u5217\u6bd4\u5bf9\u3001\u56fe\u6784\u5efa\u6216\u5e73\u6ed1\uff0c\u4e5f\u4e0d\u80fd\u636e\u6b64\u51b3\u5b9a\u771f\u5b9e\u7269\u79cd\u5e94\u5206\u51e0\u7ec4\u3002<\/p>\n<figure class=\"guide-figure\" style=\"margin:24px 0 28px\"><img loading=\"lazy\" decoding=\"async\" src=\"\/wordpress\/wp-content\/uploads\/2026\/11\/pggb-partition-alignment-length-weight-community-contigs-guide.png\" alt=\"\u53ea\u6539\u4e00\u6761\u8fb9\uff0c\u5206\u533a\u53d8\u6210\u4e09\u4e2a\u3002\u516d\u6761\u7ec4\u5185\u6bd4\u5bf9\u4fdd\u6301\u4e00\u81f4\uff0c\u72ec\u7acb\u6539\u53d8\u4e00\u6761\u8de8\u67d3\u8272\u4f53\u7684\u6bd4\u5bf9\u3002\u5f31\u8de8\u7ec4\u8fb9\uff0c1000 bp \u00d7 99% = 990\uff0c\u4e24\u7ec4\u5404\u4e09\u6761\uff0c\u6309\u67d3\u8272\u4f53\u53f7\u805a\u5728\u4e00\u8d77\u3002\u5f3a\u8de8\u7ec4\u8fb9\uff0c28000 bp \u00d7 99% = 27720\uff0c\u4e09\u7ec4\u5404\u4e24\u6761\uff0cC \u7684\u4e24\u6761\u67d3\u8272\u4f53\u5355\u72ec\u805a\u5728\u4e00\u8d77\u3002\u8f93\u5165\u6838\u5bf9\uff0c\u6ca1\u6709\u6bd4\u5bf9\u7684\u7b2c\u4e03\u6761\u5e8f\u5217\uff0c\u4e0d\u4f1a\u51fa\u73b0\u5728\u8fd9\u4e24\u4e2a\u811a\u672c\u751f\u6210\u7684\u6210\u5458\u6e05\u5355\u5185\u3002\" width=\"1200\" height=\"840\" style=\"display:block;width:100%;height:auto;border-radius:10px\"><figcaption style=\"font-size:14px;line-height:1.6;margin:9px 2px 0;color:#475569\">\u516d\u6761\u7ec4\u5185\u6bd4\u5bf9\u4fdd\u6301\u4e00\u81f4\uff0c\u72ec\u7acb\u6539\u53d8\u4e00\u6761\u8de8\u67d3\u8272\u4f53\u7684\u6bd4\u5bf9\u3002<\/figcaption><\/figure>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u5c11\u6389\u7684\u7b2c\u4e03\u6761\u5e8f\u5217\u53bb\u4e86\u54ea\u91cc<\/h2>\n<p>\u4e24\u7ec4\u5b9e\u9a8c\u7684\u8fb9\u6587\u4ef6\u91cc\u90fd\u53ea\u6709\u516d\u4e2a\u9876\u70b9\u3002\u90a3\u6761\u989d\u5916\u7684\u7ec4\u4ef6\u5728\u539f\u59cb\u6e05\u5355\u91cc\u6709\u540d\u5b57\uff0c\u5374\u6ca1\u6709\u5728\u6bd4\u5bf9\u7684\u67e5\u8be2\u5217\u6216\u76ee\u6807\u5217\u51fa\u73b0\u3002\u8f6c\u6362\u811a\u672c\u901a\u8fc7\u626b\u63cf\u8fd9\u4e24\u5217\u5efa\u7acb\u9876\u70b9\u7f16\u53f7\uff0c\u7ed3\u679c\u5b83\u6ca1\u6709\u8fdb\u5165\u793e\u533a\u68c0\u6d4b\uff0c\u5f53\u7136\u4e5f\u4e0d\u4f1a\u51fa\u73b0\u5728\u4efb\u4f55\u793e\u533a\u6210\u5458\u6e05\u5355\u91cc\u3002\u5982\u679c\u4ec5\u68c0\u67e5\u6bcf\u4e2a\u793e\u533a\u4e2d\u7684\u5e8f\u5217\u90fd\u80fd\u5728\u539f\u59cb FASTA \u627e\u5230\uff0c\u6574\u5957\u68c0\u67e5\u53ef\u4ee5\u770b\u4f3c\u901a\u8fc7\uff0c\u4f46\u8f93\u5165\u4e0e\u8f93\u51fa\u5e76\u6ca1\u6709\u5b9e\u73b0\u53cc\u5411\u6838\u5bf9\u3002\u8fd8\u5e94\u53cd\u8fc7\u6765\u7528\u539f\u59cb\u5e8f\u5217\u540d\u51cf\u53bb\u6240\u6709\u793e\u533a\u6210\u5458\uff0c\u5206\u522b\u6c47\u603b\u9057\u6f0f\u7ec4\u4ef6\u7684\u6570\u91cf\u4e0e\u78b1\u57fa\u603b\u6570\u3002<\/p>\n<pre style=\"max-width:100%;box-sizing:border-box;overflow-x:auto;margin:18px 0;padding:14px 16px;background:#f3f6fa;color:#1a293c;border:1px solid #d8e1ea;border-radius:8px;line-height:1.55;white-space:pre;overflow-wrap:normal;word-break:normal\"><code class=\"language-bash\">python3 scripts\/paf2net.py -p align.paf\r\npython3 scripts\/net2communities.py \\\r\n  -e align.paf.edges.list.txt -w align.paf.edges.weights.txt \\\r\n  -n align.paf.vertices.id2name.txt --output-prefix groups\r\n<\/code><\/pre>\n<p>\u8bfb\u8005\u62ff\u81ea\u5df1\u7684\u6570\u636e\u590d\u67e5\u65f6\uff0c\u5e94\u5148\u786e\u8ba4\u6bd4\u5bf9\u6587\u4ef6\u6765\u81ea\u9884\u671f\u7684\u5de5\u5177\u548c\u9636\u6bb5\u3002\u8fd9\u4e2a\u7248\u672c\u7684\u8f6c\u6362\u811a\u672c\u4ece\u524d\u5341\u4e09\u4e2a\u5b57\u6bb5\u53d6\u67e5\u8be2\u540d\u3001\u76ee\u6807\u540d\u3001\u6bd4\u5bf9\u957f\u5ea6\u548c\u4e00\u81f4\u6027\uff0c\u6309\u767e\u5206\u5236\u89e3\u6790\u4e00\u81f4\u6027\u503c\u3002\u4e0d\u540c\u5de5\u5177\u8f93\u51fa\u7684 PAF 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style=\"color:#905321;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2026\/11\/ysx-bioinformatics-practice-074-085-b0103eb15d21.zip\">\u4e0b\u8f7d\u672c\u7bc7\u5b9e\u9a8c\u811a\u672c\u4e0e\u7ed3\u679c\uff0812 \u7bc7\u5408\u96c6 ZIP\uff09<\/a>\uff0c\u89e3\u538b\u540e\u6253\u5f00 <code>084-pggb<\/code> \u76ee\u5f55\u3002<\/p>\n<p class=\"guide-end\" style=\"margin-top:1.6em;padding-top:1.0em;border-top:1px solid #d7e0e9\">\u591a\u4e2a\u7ec4\u88c5\u9700\u8981\u53cd\u590d\u6bd4\u8f83\u5206\u533a\u524d\u540e\u7684\u6bd4\u5bf9\u548c\u6210\u5458\u6e05\u5355\u65f6\uff0c\u53ef\u4ee5\u5728<a data-ysx-event=\"contact_click\" style=\"color:#905321;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/www.biocloudservice.com\/wordpress\/compute-services\/shared-research-workspace\/\">\u4e91\u751f\u4fe1\u7684\u751f\u7269\u4fe1\u606f\u5206\u6790\u670d\u52a1\u5668<\/a>\u6309\u7248\u672c\u4fdd\u7559\u6bd4\u5bf9\u4e0e\u5efa\u56fe\u8f93\u5165\u3002<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>\u7528\u540c\u4e00\u7ec4\u67d3\u8272\u4f53\u540d\u79f0\u5b9e\u9645\u8fd0\u884c PGGB 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