{"id":1510,"date":"2025-04-17T11:17:29","date_gmt":"2025-04-17T03:17:29","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1510"},"modified":"2025-04-17T16:32:37","modified_gmt":"2025-04-17T08:32:37","slug":"pggb%e6%9e%84%e5%bb%ba%e5%9b%be%e5%bd%a2%e6%b3%9b%e5%9f%ba%e5%9b%a0%e7%bb%84","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/04\/17\/pggb%e6%9e%84%e5%bb%ba%e5%9b%be%e5%bd%a2%e6%b3%9b%e5%9f%ba%e5%9b%a0%e7%bb%84\/","title":{"rendered":"Pggb\u6784\u5efa\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1510\" class=\"elementor elementor-1510\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-a008d15 e-con-full e-flex e-con e-parent\" data-id=\"a008d15\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-f423034 elementor-widget elementor-widget-heading\" data-id=\"f423034\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">PGGB\u6784\u5efa\u6cdb\u57fa\u56e0\u7ec4<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5d37759 elementor-widget elementor-widget-heading\" data-id=\"5d37759\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. \u524d\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1730e9d elementor-widget elementor-widget-text-editor\" data-id=\"1730e9d\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8001\u89c4\u77e9\uff0c\u6b63\u5f0f\u5f00\u59cb\u4e4b\u524d\u8fd8\u662f\u8bf4\u4e00\u4e0b\u4e3a\u4ec0\u4e48\u9009\u62e9\u7528PGGB\u6784\u5efa\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u3002\u5176\u5b9e\u5728\u7528PGGB\u4e4b\u524d\u6211\u5c1d\u8bd5\u8fc7\u5f88\u591a\u4e2a\u6784\u5efa\u56fe\u6cdb\u7684\u8f6f\u4ef6\uff0c\u6bd4\u5982\u8bf4Minigraph\u6216\u8005minimap+syri\u4ee5\u53ca\u4e00\u4e9b\u5176\u4ed6\u7684\u884d\u751f\u6d41\u7a0b\uff0c\u4f46\u662f\u6548\u679c\u90fd\u4e0d\u592a\u597d\u3002\u524d\u51e0\u5929\u5076\u7136\u4f7f\u7528PGGB\u8bd5\u4e86\u4e00\u4e0b\u8fd8\u4e0d\u9519\uff0c\u53ef\u4ee5\u63a8\u8350\u4e00\u4e0b\uff01<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-145a60d elementor-widget elementor-widget-heading\" data-id=\"145a60d\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. \u8f6f\u4ef6\u5b89\u88c5<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c43f931 elementor-widget elementor-widget-text-editor\" data-id=\"c43f931\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p># \u4e0b\u8f7dPGGB<\/p><p>mamba create -n pggb\u00a0<\/p><p>mamba activate pggb<\/p><p>mamba install -c bioconda -c conda-forge pggb<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-262cdcc elementor-widget elementor-widget-heading\" data-id=\"262cdcc\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. \u51c6\u5907\u6570\u636e<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3d7687b elementor-widget elementor-widget-heading\" data-id=\"3d7687b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.1 \u57fa\u56e0\u7ec4\u6309\u67d3\u8272\u4f53\u6c34\u5e73\u62c6\u5206<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-91c5f5c elementor-widget elementor-widget-text-editor\" data-id=\"91c5f5c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>PGGB\u5b98\u65b9\u6587\u6863\u63a8\u8350\u628a\u6574\u4e2a\u57fa\u56e0\u7ec4\u6309\u7167\u67d3\u8272\u4f53\u5212\u5206\uff0c\u968f\u540e\u4ee5\u67d3\u8272\u4f53\u4e3a\u5355\u4f4d\u6784\u5efa\u56fe\u6cdb\uff0c\u6bcf\u4e2a\u4eba\u5bf9\u5e8f\u5217\u7684\u547d\u540d\u65b9\u5f0f\u90fd\u4e0d\u540c\uff0c\u56e0\u6b64\u8fd9\u91cc\u5c31\u4e0d\u4e0a\u4ee3\u7801\u4e86\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-12f004e elementor-widget elementor-widget-heading\" data-id=\"12f004e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.2 \u67d3\u8272\u4f53ID\u91cd\u547d\u540d<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-622bf69 elementor-widget elementor-widget-text-editor\" data-id=\"622bf69\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>PGGB\u5efa\u8bae\u67d3\u8272\u4f53\u7684ID\u4e25\u683c\u9075\u5faaPanSN-spec\u89c4\u5b9a\u7684\u683c\u5f0f\uff0c\u5177\u4f53\u89c4\u5219\u4e3a\uff0c[sample_name][delim][haplotype_id][delim][contig_or_scaffold_name]\u3002<strong><span style=\"color: #ff0000;\">\u8bf4\u4eba\u8bdd\u7248\u672c\uff0c\u5176\u5b9e\u5c31\u662f\u7269\u79cd\u540d+\u5355\u500d\u578bid+\u67d3\u8272\u4f53id\uff0c\u7136\u540e\u4e2d\u95f4\u7528#\u8fde\u63a5\u3002\u4f8b\u5982\uff0c\u62df\u5357\u82a5\u7684\u4e00\u53f7\u67d3\u8272\u4f53\u5c31\u53ef\u4ee5\u547d\u540d\u4e3a\uff1a<span class=\"font20\"><b>Arabidopsis_<\/b><\/span><span class=\"font20\"><b>thaliana#1#Chr1\uff0cArabidopsis_thaliana\u5bf9\u5e94[sample_name]\uff0c1\u5bf9\u5e94[haplotype_id]\uff0cChr1\u5bf9\u5e94[contig_or_scaffold_name]\u3002<\/b><\/span><\/span><\/strong><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-215d473 elementor-widget elementor-widget-heading\" data-id=\"215d473\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">4. \u8fd0\u884cPGGB<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-cdd88b2 elementor-widget elementor-widget-text-editor\" data-id=\"cdd88b2\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>pggb -i in.fa \\ # input file in FASTA format<br \/>-o output \\ # output directory<br \/>-t 16 \\ # number of threads<br \/>-p 90 \\ # minimum average nucleotide identity for segments<br \/>-s 5k \\ # segment length for scaffolding the graph<br \/>-V &#8216;ref:1000&#8217; # make a VCF against &#8220;ref&#8221; decomposing variants &lt;= 1000bp<\/p><p># -o \u8f93\u51fa\u6587\u4ef6\u5939<\/p><p># -p \u8fd9\u4e2a\u53c2\u6570\u53ef\u4ee5\u7406\u89e3\u4e3a\u4e24\u4e2a\u6bd4\u5bf9\u4e0a\u7684\u7247\u6bb5\u7684\u76f8\u4f3c\u5ea6\u7684\u9608\u503c<\/p><p># -s \u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684\u7247\u6bb5\u957f\u5ea6<\/p><p># -V \u8fd9\u4e00\u6b65\u662f\u8c03\u7528vg\u4ecegfa\u6587\u4ef6\u62c6\u5206\u51fa\u6765vcf\u6587\u4ef6\uff0c\u6307\u5b9a\u53c2\u8003\u57fa\u56e0\u7ec4\u548c\u6700\u5927\u7684\u53d8\u5f02\u957f\u5ea6<\/p><p>\u00a0<\/p><p># \u8f93\u51fa\u6587\u4ef6<\/p><p>*seqwish.gfa \u539f\u59cb\u7684gfa\u683c\u5f0f\u7684\u56fe\u6cdb<\/p><p>*smooth.final.gfa \u538b\u7f29\u540e\u7684gfa\u683c\u5f0f\u7684\u56fe\u6cdb\uff0c\u4e00\u822c\u4f5c\u4e3a\u540e\u7eed\u5206\u6790\u4f7f\u7528<\/p><p>\u00a0<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b62a702 elementor-widget elementor-widget-text-editor\" data-id=\"b62a702\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd9\u91cc\u9700\u8981\u5f3a\u8c03\u4e00\u4e9b\u6bd4\u8f83\u91cd\u8981\u7684\u53c2\u6570\uff1a<span style=\"color: #ff0000;\">-p<\/span> \u867d\u7136\u8fd9\u4e2a\u662f\u4e24\u4e2a\u7247\u6bb5\u76f8\u4f3c\u5ea6\u7684\u9608\u503c\uff0c\u4f46\u662f\u672c\u8d28\u4e0a\u662f\u4e0d\u540c\u7269\u79cd\u4e4b\u95f4\u7684\u53d8\u5f02\u7a0b\u5ea6\uff0c\u53d8\u5f02\u7a0b\u5ea6\u8d8a\u5927\u9608\u503c\u5c31\u5e94\u8be5\u8bbe\u7f6e\u7684\u8d8a\u5c0f\uff0c\u5982\u679c\u53d8\u5f02\u7a0b\u5ea6\u5f88\u9ad8\uff0c\u5e76\u4e14\u8bbe\u7f6e\u4e86\u8f83\u9ad8\u7684\u9608\u503c\u4f1a\u5bfc\u81f4\u6700\u540e\u6784\u5efa\u51fa\u6765\u7684\u56fe\u6cdb\u4e2d\u7684SV\u5f88\u5c11\uff1b<span style=\"color: #ff0000;\">-s <span style=\"color: #000000;\">\u56fe\u6cdb\u4e2d\u7247\u6bb5\u7684\u5927\u5c0f\uff0c\u540c\u4e0a\u4e5f\u662f\u8d8a\u5c0fSV\u8d8a\u591a<\/span><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>PGGB\u6784\u5efa\u6cdb\u57fa\u56e0\u7ec4 1. \u524d\u8a00 \u8001\u89c4\u77e9\uff0c\u6b63\u5f0f\u5f00\u59cb\u4e4b\u524d\u8fd8\u662f\u8bf4\u4e00\u4e0b\u4e3a\u4ec0\u4e48\u9009\u62e9\u7528PGGB\u6784\u5efa\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u3002\u5176\u5b9e\u5728\u7528 &#8230; <a title=\"Pggb\u6784\u5efa\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/04\/17\/pggb%e6%9e%84%e5%bb%ba%e5%9b%be%e5%bd%a2%e6%b3%9b%e5%9f%ba%e5%9b%a0%e7%bb%84\/\" aria-label=\"\u9605\u8bfb Pggb\u6784\u5efa\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-1510","post","type-post","status-publish","format-standard","hentry","category-6"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - 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