{"id":3029,"date":"2026-03-07T21:09:02","date_gmt":"2026-03-07T13:09:02","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=3029"},"modified":"2026-03-07T21:45:00","modified_gmt":"2026-03-07T13:45:00","slug":"%e8%ae%b0%e5%bd%95%e4%b8%80%e6%ac%a1%e8%a1%a5gap%e7%9a%84%e6%b5%81%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2026\/03\/07\/%e8%ae%b0%e5%bd%95%e4%b8%80%e6%ac%a1%e8%a1%a5gap%e7%9a%84%e6%b5%81%e7%a8%8b\/","title":{"rendered":"\u8bb0\u5f55\u4e00\u6b21\u8865Gap\u7684\u6d41\u7a0b"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"3029\" class=\"elementor elementor-3029\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-3a2dad6 e-flex e-con-boxed e-con e-parent\" data-id=\"3a2dad6\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-eae50fa elementor-widget elementor-widget-heading\" data-id=\"eae50fa\" 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\">\u5f15\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-03eebef elementor-widget elementor-widget-text-editor\" data-id=\"03eebef\" 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>\u8bb0\u5f55\u4e00\u6b21\u4f7f\u7528quarTeT+TGS-GapCloser+Gapsuite\u8865\u57fa\u56e0\u7ec4gap\u7684\u8fc7\u7a0b\uff0c\u7eaf\u8bb0\u5f55\u6587\u7ae0\uff0c\u53ea\u6709\u6d41\u7a0b\u7684\u63cf\u8ff0\uff0c\u4e0d\u4f1a\u6709\u4efb\u4f55\u539f\u7406\u7684\u8bb2\u89e3\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-9bd5e0f elementor-widget elementor-widget-heading\" data-id=\"9bd5e0f\" 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\">\u5b89\u88c5\u8f6f\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-722927f elementor-widget elementor-widget-code-highlight\" data-id=\"722927f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp># quarTeT\nconda create -n gapfill --channel conda-forge --channel bioconda python=3.11.4 minimap2=2.26 mummer4=4.0.0rc1 trf=4.09.1 cd-hit=4.8.1 blast=2.14.0 tidk=0.2.31 r=4.3 r-rideogram=0.2.2 r-ggplot2=3.4.4 gnuplot=5.4 unimap=0.1\ngit clone https:\/\/github.com\/aaranyue\/quarTeT\n# mm2plus\nmamba install bioconda::mm2plus\n# TGS-GapCloser\nmamba install bioconda::tgsgapcloser\n# Gapsuite\nmamba install bioconda::jellyfish\nmamba install bioconda::seqkit\ngit clone https:\/\/github.com\/panlab-bioinfo\/RAfilter.git\ncd RAfilter\/src\nmake\n\n\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8fc3ecf elementor-widget elementor-widget-heading\" data-id=\"8fc3ecf\" 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\">\u586b\u8865Gap<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6c13819 elementor-widget elementor-widget-text-editor\" data-id=\"6c13819\" 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>hifi\u6570\u636e\u7684bam\u6587\u4ef6\u8f6cfa<\/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-0042d87 elementor-widget elementor-widget-code-highlight\" data-id=\"0042d87\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>pbindex ccs.bam\nbam2fasta -o out ccs.bam<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-927f17f elementor-widget elementor-widget-text-editor\" data-id=\"927f17f\" 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>ont\u7684\u6d4b\u5e8f\u6570\u636efq\u8f6c\u4e3afa<\/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-f82595c elementor-widget elementor-widget-code-highlight\" data-id=\"f82595c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>seqkit fq2fa -j 50 pass.raw.fq > pass.raw.fa<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7ac4232 elementor-widget elementor-widget-text-editor\" data-id=\"7ac4232\" 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>quarTeT\u521d\u6b65\u586b\u8865gap<\/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-b8f8656 elementor-widget elementor-widget-code-highlight\" data-id=\"b8f8656\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>python ~\/Software\/quarTeT\/quartet.py GapFiller \\\n-d all_ont_fill.genome.filled.fasta \\\n-g out.fasta hifiasm.hic.haps.p_ctg.gfa.fa pass.raw.fa \\\n-t 60 -p all_ont_hifi_fill<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3cf41b5 elementor-widget elementor-widget-text-editor\" data-id=\"3cf41b5\" 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>TGS-GapCloser\u518d\u6b21\u586b\u8865<\/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-d420a54 elementor-widget elementor-widget-code-highlight\" data-id=\"d420a54\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>tgsgapcloser --scaff all_ont_hifi_fill.genome.filled.chr10a.fasta \\\n--reads pass.raw.fa \\\n--output tgsgapcloser_ont --ne<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-27eb79d elementor-widget elementor-widget-code-highlight\" data-id=\"27eb79d\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>tgsgapcloser --scaff all_ont_hifi_fill.genome.filled.chr10a.fasta \\\n--reads  out.fasta \\\n--output tgsgapcloser_ont --ne<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f9c3d97 elementor-widget elementor-widget-text-editor\" data-id=\"f9c3d97\" 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\u4e00\u6b65\u7ed3\u675f\uff0c\u53ea\u67091\u4e2agap\u6ca1\u6709\u88ab\u8865\u4e0a\uff0c\u968f\u540e\u4f7f\u7528Gapsuite\u624b\u52a8\u586b\u8865\u3002Gapsuite\u4ea7\u751f\u7684\u6587\u4ef6\u5f88\u5927\uff0c\u56e0\u6b64\u6211\u4eec\u53ea\u63d0\u53d6\u5b58\u5728gap\u7684\u67d3\u8272\u4f53\u8dd1Gapsuite\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-2850510 elementor-widget elementor-widget-code-highlight\" data-id=\"2850510\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>seqkit grep -p  \"chr10a\" all_ont_hifi_fill.genome.filled.fasta > all_ont_hifi_fill.genome.filled.chr10a.fasta<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-24fd9d3 elementor-widget elementor-widget-text-editor\" data-id=\"24fd9d3\" 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>Gapsuite\u624b\u52a8\u8865gap<\/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-fabdcb7 elementor-widget elementor-widget-code-highlight\" data-id=\"fabdcb7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>bash pipeline.sh -r ont -t 60 all_ont_hifi_fill.genome.filled.chr10a.fasta pass.raw.fa<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\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>\u5f15\u8a00 \u8bb0\u5f55\u4e00\u6b21\u4f7f\u7528quarTeT+TGS-GapCloser+Gapsuite\u8865\u57fa\u56e0\u7ec4gap\u7684\u8fc7\u7a0b\uff0c\u7eaf\u8bb0\u5f55\u6587\u7ae0 &#8230; <a title=\"\u8bb0\u5f55\u4e00\u6b21\u8865Gap\u7684\u6d41\u7a0b\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2026\/03\/07\/%e8%ae%b0%e5%bd%95%e4%b8%80%e6%ac%a1%e8%a1%a5gap%e7%9a%84%e6%b5%81%e7%a8%8b\/\" aria-label=\"\u9605\u8bfb \u8bb0\u5f55\u4e00\u6b21\u8865Gap\u7684\u6d41\u7a0b\">\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-3029","post","type-post","status-publish","format-standard","hentry","category-6"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>\u8bb0\u5f55\u4e00\u6b21\u8865Gap\u7684\u6d41\u7a0b - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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