{"id":2214,"date":"2025-10-17T17:59:21","date_gmt":"2025-10-17T09:59:21","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2214"},"modified":"2025-10-17T19:24:23","modified_gmt":"2025-10-17T11:24:23","slug":"quartet%e5%9f%ba%e5%9b%a0%e7%bb%84gap%e5%a1%ab%e5%85%85%e6%a3%80%e6%b5%8b%e7%ab%af%e7%b2%92%e5%92%8c%e9%87%8d%e5%a4%8d%e5%ba%8f%e5%88%97","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/17\/quartet%e5%9f%ba%e5%9b%a0%e7%bb%84gap%e5%a1%ab%e5%85%85%e6%a3%80%e6%b5%8b%e7%ab%af%e7%b2%92%e5%92%8c%e9%87%8d%e5%a4%8d%e5%ba%8f%e5%88%97\/","title":{"rendered":"quarTeT\u57fa\u56e0\u7ec4Gap\u586b\u5145\u3001\u68c0\u6d4b\u7aef\u7c92\u548c\u91cd\u590d\u5e8f\u5217"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"2214\" class=\"elementor elementor-2214\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-cb2f425 e-flex e-con-boxed e-con e-parent\" data-id=\"cb2f425\" 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-2e78484 elementor-widget elementor-widget-heading\" data-id=\"2e78484\" 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-8ea3328 elementor-widget elementor-widget-text-editor\" data-id=\"8ea3328\" 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\u662f\u4e00\u7bc7\u8fdf\u6765\u7684\u535a\u5ba2\uff0c\u5f88\u4e45\u4e4b\u524d\u5c31\u7528\u8fc7\u8fd9\u4e2a\u8f6f\u4ef6\uff0c\u4e00\u76f4\u6ca1\u6709\u8bb0\u5f55\uff0c\u4eca\u5929\u6765\u8bb0\u5f55\u4e00\u4e0b\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-3360ac6 elementor-widget elementor-widget-heading\" data-id=\"3360ac6\" 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\u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-051215f elementor-widget elementor-widget-code-highlight\" data-id=\"051215f\" 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>mamba create -n quarTeTdependencies --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<\/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-bff9f3a elementor-widget elementor-widget-heading\" data-id=\"bff9f3a\" 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. \u8f6f\u4ef6\u4f7f\u7528<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c3f8b44 elementor-widget elementor-widget-code-highlight\" data-id=\"c3f8b44\" 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>### \u586b\u5145\u57fa\u56e0\u7ec4\u7ec4\u88c5\u4e2d\u7684\u7a7a\u9699\uff08gap\uff09\u3002\npython ~\/Software\/quarTeT\/quartet.py GapFiller -g ..\/..\/..\/..\/hap_n_12.hic.p_utg.fa -d groups.review.asm.fasta -t 30\n\n# -g ..\/..\/..\/..\/hap_n_12.hic.p_utg.fa: \u6307\u5b9a\u5305\u542b\u7a7a\u9699\uff08\u901a\u5e38\u8868\u793a\u4e3a 'N'\uff09\u7684\u57fa\u56e0\u7ec4\u8349\u56fe\u6587\u4ef6\uff08scaffold\/contig\uff09\u3002\n# -d groups.review.asm.fasta: \u6307\u5b9a\u7528\u4e8e\u586b\u5145\u7a7a\u9699\u7684\u5e8f\u5217\u6587\u4ef6\uff0c\u8fd9\u901a\u5e38\u662f unplaced contigs \u6216\u8005\u5176\u4ed6\u53ef\u4ee5\u7528\u6765\u586b\u8865\u7f3a\u53e3\u7684\u5e8f\u5217\u96c6\u5408\u3002\n# -t 30: \u6307\u5b9a\u7528\u4e8e\u6b64\u4efb\u52a1\u7684\u7ebf\u7a0b\u6570\uff0c\u4ee5\u52a0\u901f\u8ba1\u7b97\u8fc7\u7a0b\u3002\n\n### \u8bc6\u522b\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e2d\u7684\u7aef\u7c92\u533a\u57df\u3002\npython ~\/Software\/quarTeT\/quartet.py TeloExplorer -i groups.review.asm.chr.genome.fasta -c plant\n\n# -i groups.review.asm.chr.genome.fasta: \u6307\u5b9a\u8f93\u5165\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6\uff0c\u901a\u5e38\u662f\u67d3\u8272\u4f53\u7ea7\u522b\u7684\u7ec4\u88c5\u7ed3\u679c\u3002\n# -c plant: \u6307\u5b9a\u8981\u641c\u7d22\u7684\u7aef\u7c92\u91cd\u590d\u5e8f\u5217\u7684\u7c7b\u578b\u3002\u8fd9\u91cc 'plant' \u8868\u793a\u4f7f\u7528\u690d\u7269\u5178\u578b\u7684\u7aef\u7c92\u91cd\u590d\u5e8f\u5217\uff08TTTAGGG\uff09\u8fdb\u884c\u641c\u7d22\u3002\n\n### \u9884\u6d4b\u57fa\u56e0\u7ec4\u4e2d\u7684\u7740\u4e1d\u7c92\u533a\u57df\u3002\npython ~\/Software\/quarTeT\/quartet.py CentroMiner -i quarTeT.genome.filled.fasta --TE quarTeT.genome.filled.fasta.gff --gene .\/Final_result\/Prunus_pedunculata.gff3 -t 40 -p centromere_out\n\n# -i quarTeT.genome.filled.fasta: \u6307\u5b9a\u8f93\u5165\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6\uff0c\u8fd9\u91cc\u4f7f\u7528\u7684\u662f\u7ecf\u8fc7 GapFiller \u586b\u5145\u540e\u7684\u7248\u672c\u3002\n# --TE quarTeT.genome.filled.fasta.gff: \u6307\u5b9a\u8f6c\u5ea7\u5143\u4ef6\uff08Transposable Element, TE\uff09\u7684\u6ce8\u91ca\u6587\u4ef6\uff0c\u683c\u5f0f\u4e3a GFF\u3002\u7740\u4e1d\u7c92\u533a\u57df\u901a\u5e38\u5bcc\u542b\u7279\u5b9a\u7684\u8f6c\u5ea7\u5b50\uff0c\u6b64\u4fe1\u606f\u6709\u52a9\u4e8e\u9884\u6d4b\uff0c\u53ef\u4ee5\u662fEDTA\u6216Repetmasker\u8f93\u51fa\u7684gff\u6587\u4ef6\u3002\n# --gene .\/Final_result\/Prunus_pedunculata.gff3: \u6307\u5b9a\u57fa\u56e0\u6ce8\u91ca\u6587\u4ef6\uff0c\u683c\u5f0f\u4e3a GFF3\u3002\u7740\u4e1d\u7c92\u533a\u57df\u901a\u5e38\u662f\u57fa\u56e0\u7a00\u758f\u533a\uff0c\u6b64\u4fe1\u606f\u4e5f\u4f5c\u4e3a\u9884\u6d4b\u7684\u4f9d\u636e\u3002\n# -t 40: \u6307\u5b9a\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\u3002\n# -p centromere_out: \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\u6216\u8f93\u51fa\u76ee\u5f55\u7684\u540d\u79f0\u3002<\/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-c417ba7 elementor-widget elementor-widget-heading\" data-id=\"c417ba7\" 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. \u8f93\u51fa\u7ed3\u679c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a394332 elementor-widget elementor-widget-text-editor\" data-id=\"a394332\" 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.genome.filled.fasta \uff1a\u8865gap\u540e\u7684\u57fa\u56e0\u7ec4<\/p><p>quarTeT.genome.filled.detail\uff1a\u8865gap\u7684\u4fe1\u606f\u7edf\u8ba1\u6587\u4ef6<\/p><p>quarTeT.genome.filled.png\uff1a\u6838\u578b\u56fe<\/p><p>quarTeT.telo.info\uff1a\u9884\u6d4b\u7aef\u7c92\u7684\u4fe1\u606f\u7edf\u8ba1\u6587\u4ef6<\/p><p>quarTeT.telo.png\uff1a\u6838\u578b\u56fe<\/p>\t\t\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>1. \u524d\u8a00 \u8fd9\u662f\u4e00\u7bc7\u8fdf\u6765\u7684\u535a\u5ba2\uff0c\u5f88\u4e45\u4e4b\u524d\u5c31\u7528\u8fc7\u8fd9\u4e2a\u8f6f\u4ef6\uff0c\u4e00\u76f4\u6ca1\u6709\u8bb0\u5f55\uff0c\u4eca\u5929\u6765\u8bb0\u5f55\u4e00\u4e0b\u3002 2. \u8f6f\u4ef6\u4e0b\u8f7d mam &#8230; <a title=\"quarTeT\u57fa\u56e0\u7ec4Gap\u586b\u5145\u3001\u68c0\u6d4b\u7aef\u7c92\u548c\u91cd\u590d\u5e8f\u5217\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/17\/quartet%e5%9f%ba%e5%9b%a0%e7%bb%84gap%e5%a1%ab%e5%85%85%e6%a3%80%e6%b5%8b%e7%ab%af%e7%b2%92%e5%92%8c%e9%87%8d%e5%a4%8d%e5%ba%8f%e5%88%97\/\" aria-label=\"\u9605\u8bfb quarTeT\u57fa\u56e0\u7ec4Gap\u586b\u5145\u3001\u68c0\u6d4b\u7aef\u7c92\u548c\u91cd\u590d\u5e8f\u5217\">\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-2214","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>quarTeT\u57fa\u56e0\u7ec4Gap\u586b\u5145\u3001\u68c0\u6d4b\u7aef\u7c92\u548c\u91cd\u590d\u5e8f\u5217 - 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