{"id":1446,"date":"2025-03-10T11:44:54","date_gmt":"2025-03-10T03:44:54","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1446"},"modified":"2025-06-09T21:36:33","modified_gmt":"2025-06-09T13:36:33","slug":"hypiper%e5%9f%ba%e4%ba%8e%e4%ba%8c%e4%bb%a3%e6%b5%8b%e5%ba%8f%e6%95%b0%e6%8d%ae%e7%bb%84%e8%a3%85%e7%9b%b4%e7%b3%bb%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e4%bb%a5%e5%8f%8a%e4%b8%a4%e4%b8%aa%e6%b4%be","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/03\/10\/hypiper%e5%9f%ba%e4%ba%8e%e4%ba%8c%e4%bb%a3%e6%b5%8b%e5%ba%8f%e6%95%b0%e6%8d%ae%e7%bb%84%e8%a3%85%e7%9b%b4%e7%b3%bb%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e4%bb%a5%e5%8f%8a%e4%b8%a4%e4%b8%aa%e6%b4%be\/","title":{"rendered":"Hypiper\uff1a\u57fa\u4e8e\u4e8c\u4ee3\u6d4b\u5e8f\u6570\u636e\u7ec4\u88c5\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u4ee5\u53ca\u4e24\u4e2a\u6d3e\u751f\u7684pipline\uff1aHypiper-nf\u548cparagone-nf"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1446\" class=\"elementor elementor-1446\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-d9c755b e-flex e-con-boxed e-con e-parent\" data-id=\"d9c755b\" 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-af90beb elementor-widget elementor-widget-heading\" data-id=\"af90beb\" 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\">Hybpiper\u548cParagone-nf\u7684\u4f7f\u7528<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a07020a elementor-widget elementor-widget-heading\" data-id=\"a07020a\" 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-145500c elementor-widget elementor-widget-heading\" data-id=\"145500c\" 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\">1.1 Hybpiper<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8f7b959 elementor-widget elementor-widget-text-editor\" data-id=\"8f7b959\" 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><strong>\u5b98\u65b9\u4ecb\u7ecd\uff1a<\/strong>HybPiper \u4e13\u4e3a\u76ee\u6807\u5e8f\u5217\u6355\u83b7\u800c\u8bbe\u8ba1\uff0c\u5176\u4e2d DNA \u6d4b\u5e8f\u6587\u5e93\u9488\u5bf9\u611f\u5174\u8da3\u7684\u57fa\u56e0\u533a\u57df\u8fdb\u884c\u5bcc\u96c6\uff0c\u5c24\u5176\u662f\u9488\u5bf9\u7cfb\u7edf\u53d1\u80b2\u3002HybPiper \u662f\u4e00\u5957 Python \u811a\u672c\/\u6a21\u5757\uff0c\u53ef\u5305\u88c5\u548c\u8fde\u63a5\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\uff0c\u4ee5\u4fbf\u4ece\u9ad8\u901a\u91cf DNA \u6d4b\u5e8f\u8bfb\u6570\u4e2d\u63d0\u53d6\u76ee\u6807\u5e8f\u5217\u3002<\/p><p><span style=\"color: #ff0000;\"><strong>\u8bf4\u4eba\u8bdd\u7248\u672c\uff1a<\/strong><span style=\"color: #000000;\">\u5176\u5b9e\u5c31\u662f\u7ed3\u5408\u4e86\u6bd4\u5bf9\u8f6f\u4ef6\uff08Bwa Blastx Diamond\uff09+\u7ec4\u88c5\u8f6f\u4ef6\uff08Spades\uff09\uff0c\u57fa\u4e8e\u4e8c\u4ee3\u6d4b\u5e8f\u6570\u636e\u628a\u7279\u5b9a\u7684\u57fa\u56e0\u7ec4\u88c5\u51fa\u6765\u3002\u4e3e\u4e2a\u4f8b\u5b50\uff0c\u6211\u60f3\u83b7\u5f97\u62df\u5357\u82a5\u7684matK\u57fa\u56e0\uff0c\u5c31\u53ef\u4ee5\u901a\u8fc7Hybpiper\u628a\u8fd9\u4e2a\u57fa\u56e0\u7ec4\u88c5\u51fa\u6765\uff0c\u800c\u4e0d\u518d\u9700\u8981\u7ec4\u88c5\u6574\u4e2a\u53f6\u7eff\u4f53\u57fa\u56e0\u7ec4\u7136\u540e\u5728\u7ec4\u88c5\u6ce8\u91ca\u4ece\u800c\u63d0\u53d6matK\u57fa\u56e0\u3002<\/span><\/span><\/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-6afbf0c elementor-widget elementor-widget-heading\" data-id=\"6afbf0c\" 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\">1.2 Pargone-nf<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9fc2b4c elementor-widget elementor-widget-text-editor\" data-id=\"9fc2b4c\" 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><strong>\u5b98\u65b9\u4ecb\u7ecd\uff1a<\/strong>\u8be5\u6d41\u7a0b\u5229\u7528\u4e86 Yang \u548c Smith 2014 \u5e74\u5728\u6b64\u5904\u63cf\u8ff0\u548c\u5b9e\u65bd\u7684\u540c\u6e90\u6027\u89e3\u6790\uff08\u4e5f\u79f0\u4e3a\u76f4\u7cfb\u540c\u6e90\u6027\u63a8\u65ad\uff09\u65b9\u6cd5\u3002\u8fd9\u4e9b\u65b9\u6cd5\u540e\u6765\u88ab\u6539\u7f16\u4e3a\u76ee\u6807\u6355\u83b7\u6570\u636e\u96c6\u3002<\/p><p><span style=\"color: #ff0000;\"><strong>\u8bf4\u4eba\u8bdd\u7248\u672c\uff1a<\/strong><\/span>\u5229\u7528Yang &amp; Smith\u4e2d\u7684\u65b9\u6cd5\u6765\u5254\u9664\u6389Hybpiper\u7ed3\u679c\u4e2d\u7684\u65c1\u7cfb\u540c\u6e90\u57fa\u56e0\u3002\u4f5c\u8005\u5c06\u8fd9\u4e2a\u65b9\u6cd5\u5199\u6210\u4e86\u4e00\u4e2aPipline\uff0c\u53ef\u4ee5\u76f4\u63a5\u4ee5Hybpiper\u7684\u7ed3\u679c\u4f5c\u4e3a\u8f93\u5165\u6587\u4ef6\uff0c\u5f97\u5230\u5254\u9664\u65c1\u7cfb\u540c\u6e90\u57fa\u56e0\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\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-1514fc0 elementor-widget elementor-widget-heading\" data-id=\"1514fc0\" 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-89c37f7 elementor-widget elementor-widget-text-editor\" data-id=\"89c37f7\" 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>mamba create -n hybpiper<\/p><p>mamba activate hybpiper<\/p><p>#Hybpiper<\/p><p>mamba install bioconda::hybpiper<\/p><p># Paragone-nf<\/p><p>singularity pull library:\/\/chrisjackson-pellicle\/collection\/hybpiper-paragone:latest<\/p><p>git clone https:\/\/github.com\/chrisjackson-pellicle\/paragone-nf.git<\/p><p># \u4fee\u6539\u914d\u7f6e\u6587\u4ef6 paragone.config<\/p><p>\u66f4\u6539\u4e00\u4e0b\u5185\u5bb9\uff0c<br \/>container = &#8216;library:\/\/chrisjackson-pellicle\/collection\/hybpiper-paragone:latest&#8217;<\/p><p>\u66f4\u6539\u4e3a\uff0c<br \/>container = &#8216;file:\/\/+\u4e0b\u8f7d\u7684\u5bb9\u5668\u7684sif\u6587\u4ef6\u7684\u7edd\u5bf9\u8def\u5f84&#8217;\u3002<br \/>\u4f8b\u5982container = &#8216;file:\/\/\/home\/majunpeng\/Software\/hybpiper-nf\/hybpiper-paragone_latest.sif&#8217;<\/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-9dd2099 elementor-widget elementor-widget-heading\" data-id=\"9dd2099\" 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\u8fd0\u884c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f968a24 elementor-widget elementor-widget-heading\" data-id=\"f968a24\" 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 \u8fd0\u884cHybpiper<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c2c161a elementor-widget elementor-widget-text-editor\" data-id=\"c2c161a\" 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>Hybpiper \u5206\u4e3a\u591a\u4e2a\u6a21\u5757\uff0c\u5e38\u7528\u7684\u4e00\u822c\u5c31\u662f\u56db\u4e2a\u6a21\u5757\uff0c\u5373\uff0cassemble\uff08\u7ec4\u88c5\uff09+stats\uff08\u7edf\u8ba1\u7ec4\u88c5\u60c5\u51b5\uff09+recovery_heatmap\uff08\u53ef\u89c6\u5316\u57fa\u56e0\u6062\u590d\u60c5\u51b5\uff09+paralog_retriever\uff08\u6536\u96c6\u6bcf\u4e2a\u57fa\u56e0\u7684\u7684\u65c1\u7cfb\u540c\u6e90\u57fa\u56e0\u5e76\u4e14\u7ed8\u5236\u62f7\u8d1d\u6570\u7684\u70ed\u56fe\uff09\u3002<\/p><p>\u9996\u5148\u8981\u51c6\u5907\u8f93\u5165\u6587\u4ef6<strong>\uff08\u6700\u9ebb\u70e6\u7684\u4e00\u6b65\uff0cHybpiper\u5bf9\u8f93\u51fa\u6587\u4ef6\u7684\u683c\u5f0f\u8981\u6c42\u5f88\u4e25\u683c\uff09<\/strong>\u3002<\/p><p>\uff081\uff09\u4e8c\u4ee3\u6d4b\u5e8f\u6570\u636e\u6587\u4ef6<strong>\uff08\u53ef\u4ee5\u662f\u5168\u57fa\u56e0\u7ec4\u6d4b\u5e8f\u7684DNA\u6570\u636e\uff0c\u4e5f\u53ef\u4ee5\u662fRNA-seq\uff09<\/strong>\uff0c\u6587\u4ef6\u540d\u4e2d\u53ea\u80fd\u51fa\u73b0\u4e00\u6b21\u533a\u5206\u53cc\u7aef\u6570\u636e\u4f7f\u7528\u7684\u4e0b\u5212\u7ebf\uff0c\u5e76\u4e14\u4e0b\u5212\u7ebf\u4e4b\u524d\u7684\u5b57\u7b26\u4e32\u4f1a\u81ea\u52a8\u88ab\u8bc6\u522b\u4e3a\u6837\u672c\u7684\u540d\u5b57\u3002\u4f8b\u5982\uff0cSample1_1.fa.gz\uff0c\u6837\u672c\u540d\u4f1a\u88ab\u8bc6\u522b\u4e3aSample1\u3002<\/p><p>\uff082\uff09\u76ee\u6807\u57fa\u56e0<strong>\uff08\u4f60\u60f3\u7ec4\u88c5\u51fa\u6765\u7684\u57fa\u56e0\u7684\u53c2\u8003\u6587\u4ef6\uff0c<span style=\"color: #ff0000;\">\u5982\u679c\u60f3\u7ec4\u88c5\u51fa\u6765\u591a\u4e2a\u57fa\u56e0\uff0c\u8bf7cat\u5230\u4e00\u4e2a\u6587\u4ef6\uff0c<\/span>\u4e00\u822c\u9009\u62e9\u8fd1\u7f18\u7269\u79cd\u7684\u57fa\u56e0\u4f5c\u4e3a\u53c2\u8003\u57fa\u56e0\uff0c\u53ef\u4ee5\u6709\u628a\u591a\u4e2a\u7269\u79cd\u7684\u57fa\u56e0cat\u5230\u4e00\u8d77\uff0c\u8f6f\u4ef6\u4f1a\u81ea\u52a8\u9009\u62e9\u4e00\u4e2a\u76f8\u4f3c\u6027\u6700\u9ad8\u7684\u4f5c\u4e3a\u53c2\u8003\u57fa\u56e0\u7ec4\u8fdb\u884c\u7ec4\u88c5\uff09\u3002<\/strong>\u76ee\u6807\u6587\u4ef6\u7684\u8981\u6c42\u540c\u6837\u5201\u94bb\uff0c\u57fa\u56e0ID\u5fc5\u987b\u662f\u201cTaxon-Genename\u201d\uff0c\u5373\u6837\u672c\u540d+\u57fa\u56e0\u540d\u5b57\u3002\u4f8b\u5982Sample-Gene1\uff0c\u8f6f\u4ef6\u4f1a\u81ea\u52a8\u628aSample\u8bc6\u522b\u4e3a\u6837\u672c\u540d\uff0cGene1\u88ab\u8bc6\u522b\u4e3a\u57fa\u56e0\u540d\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-eb708d2 elementor-widget elementor-widget-text-editor\" data-id=\"eb708d2\" 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>hybpiper assemble -r ~\/sda2\/Hybpiper\/Fastq_dir\/Chrysanthemum-dichroum-RNA_1_RNA_clean.fq.gz ~\/sda2\/Hybpiper\/Fastq_dir\/Chrysanthemum-dichroum-RNA_2_RNA_clean.fq.gz -t_dna Chr_2.fasta &#8211;bwa &#8211;cpu 100<\/p><p>###\u00a0<\/p><p>-r \u4e8c\u4ee3\u6d4b\u5e8f\u6587\u4ef6<\/p><p>&#8211;bwa \u6bd4\u5bf9\u8f6f\u4ef6\u8bbe\u7f6e\u4e3abwa<\/p><p>&#8211;cpu \u6bd4\u5bf9\u8f6f\u4ef6\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570<\/p><p>-t_dna \u76ee\u6807\u57fa\u56e0\u6587\u4ef6<\/p><p>###<\/p><p><span style=\"color: #ff0000;\"><strong>\u4ee5\u4e0b\u4e3a\u5168\u90e8\u7684\u53c2\u6570<\/strong><\/span><\/p><p>###<\/p><p><strong>\u5fc5\u9009\u8f93\u5165<\/strong><br \/>&#8211;readfiles READFILES [READFILES &#8230;]\uff1a\u6307\u5b9a\u8f93\u5165\u6d4b\u5e8f\u6587\u4ef6\uff08FASTQ\u683c\u5f0f\uff09\u3002\u82e5\u63d0\u4f9b\u4e24\u4e2a\u6587\u4ef6\uff0c\u89c6\u4e3a\u53cc\u7aef\u6d4b\u5e8f\u6570\u636e\uff08R1\u548cR2\uff09\u3002\u4f8b\u5982\uff1a&#8211;readfiles sample_R1.fq sample_R2.fq\u3002<br \/>&#8211;targetfile_dna TARGETFILE_DNA\uff1a\u6838\u82f7\u9178\u9776\u6807\u6587\u4ef6\uff08FASTA\u683c\u5f0f\uff09\uff0c\u7528\u4e8eBWA\u6bd4\u5bf9\u3002\u5e8f\u5217\u5934\u683c\u5f0f\u9700\u4e3a&gt;TaxonID-geneName\uff08\u5982&gt;Human-ITS\uff09\u3002<br \/>&#8211;targetfile_aa TARGETFILE_AA\uff1a\u6c28\u57fa\u9178\u9776\u6807\u6587\u4ef6\uff08FASTA\u683c\u5f0f\uff09\uff0c\u7528\u4e8eDIAMOND\u6bd4\u5bf9\uff0c\u9002\u7528\u4e8e\u8de8\u7269\u79cd\u5206\u6790\u6216RNA\u6570\u636e\u3002<\/p><p><strong>\u53ef\u9009\u8f93\u5165<\/strong><br \/>&#8211;unpaired UNPAIRED\uff1a\u6dfb\u52a0\u5355\u7aef\u8bfb\u6bb5\u6587\u4ef6\uff0c\u4e0e\u53cc\u7aef\u6570\u636e\u8054\u5408\u4f7f\u7528\u3002\u4f8b\u5982\uff1a&#8211;unpaired sample_single.fq\u3002<\/p><p><strong>\u8bfb\u6bb5\u6bd4\u5bf9\u9009\u9879<\/strong><br \/>&#8211;bwa\uff1a\u4f7f\u7528BWA\u8fdb\u884c\u6838\u82f7\u9178\u6bd4\u5bf9\uff08\u9700&#8211;targetfile_dna\uff09\uff0c\u9002\u7528\u4e8e\u9ad8\u76f8\u4f3c\u5ea6\u9776\u6807\uff08\u5982\u79cd\u5185\u63a2\u9488\uff09\u3002<br \/>&#8211;diamond\uff1a\u4f7f\u7528DIAMOND\u8fdb\u884c\u6c28\u57fa\u9178\u6bd4\u5bf9\uff08\u9700&#8211;targetfile_aa\uff09\uff0c\u9002\u5408\u8de8\u7269\u79cd\u5206\u6790\u3002<br \/>&#8211;diamond_sensitivity\uff1a\u8c03\u6574DIAMOND\u6bd4\u5bf9\u654f\u611f\u5ea6\uff0c\u9009\u9879\u5305\u62ecmid-sensitive\u5230ultra-sensitive\uff0c\u9ed8\u8ba4\u4e2d\u7b49\u654f\u611f\u5ea6\u3002\u5efa\u8bae\u9ad8\u7075\u654f\u5ea6\u6a21\u5f0f\uff08\u5982ultra-sensitive\uff09\u63d0\u9ad8\u6bd4\u5bf9\u7387\u3002<br \/>&#8211;evalue\uff1aBLASTx\/DIAMOND\u6bd4\u5bf9\u7684e\u503c\u9608\u503c\uff0c\u9ed8\u8ba40.0001\u3002\u964d\u4f4e\u81f31e-5\u53ef\u51cf\u5c11\u5047\u9633\u6027\u3002<br \/>&#8211;max_target_seqs\uff1a\u4fdd\u7559\u7684\u6bd4\u5bf9\u76ee\u6807\u5e8f\u5217\u6570\uff0c\u9ed8\u8ba410\u3002<\/p><p><strong>\u8bfb\u6bb5\u5206\u53d1\u9009\u9879<\/strong><br \/>&#8211;distribute_low_mem\uff1a\u542f\u7528\u4f4e\u5185\u5b58\u6a21\u5f0f\uff0c\u964d\u4f4e\u5185\u5b58\u5360\u7528\u4f46\u901f\u5ea6\u51cf\u616240-50%\uff0c\u9002\u5408\u5927\u89c4\u6a21\u6570\u636e\u96c6\u3002<\/p><p><strong>\u7ec4\u88c5\u9009\u9879<\/strong><br \/>&#8211;cov_cutoff\uff1aSPAdes\u8986\u76d6\u5ea6\u9608\u503c\uff0c\u9ed8\u8ba48\u3002\u4f4e\u8986\u76d6\u6570\u636e\u53ef\u964d\u81f35\uff0c\u9ad8\u8986\u76d6\u6570\u636e\u53ef\u63d0\u9ad8\u81f310\u3002<br \/>&#8211;single_cell_assembly\uff1a\u542f\u7528\u5355\u7ec6\u80de\u6a21\u5f0f\uff08MDA\u6269\u589e\u6570\u636e\uff09\uff0c\u9002\u7528\u4e8e\u5fae\u91cfDNA\u6837\u672c\u3002<br \/>&#8211;kvals\uff1a\u624b\u52a8\u6307\u5b9aSPAdes\u7684k-mer\u503c\uff08\u9ed8\u8ba4\u81ea\u52a8\u9009\u62e9\uff09\uff0c\u4f8b\u5982&#8211;kvals 21,33,55\u3002<br \/>&#8211;merged\uff1a\u5408\u5e76\u53cc\u7aef\u8bfb\u6bb5\u540e\u7ec4\u88c5\uff0c\u63d0\u5347\u957f\u7247\u6bb5\u91cd\u5efa\u80fd\u529b\u3002<br \/>&#8211;timeout_assemble_reads\uff1a\u7ec8\u6b62\u8017\u65f6\u8d85\u8fc7\u5e73\u5747\u65f6\u95f4X%\u7684\u57fa\u56e0\u7ec4\u88c5\u4efb\u52a1\u3002<\/p><p><strong>Contig\u63d0\u53d6\u9009\u9879<\/strong><br \/>&#8211;not_protein_coding\uff1a\u4f7f\u7528BLASTn\u4ee3\u66ffExonerate\u63d0\u53d6\u975e\u7f16\u7801\u57fa\u56e0\u7684contig\u3002<br \/>&#8211;thresh\uff1a\u4fdd\u7559\u6bd4\u5bf9\u7684\u6700\u4f4e\u76f8\u4f3c\u5ea6\uff0c\u9ed8\u8ba455%\u3002Exonerate\u57fa\u4e8e\u6c28\u57fa\u9178\uff0cBLASTn\u57fa\u4e8e\u6838\u82f7\u9178\u3002<br \/>&#8211;extract_contigs_blast_evalue\uff1aBLASTn\u7684e\u503c\u9608\u503c\uff0c\u9ed8\u8ba410\u3002<br \/>&#8211;paralog_min_length_percentage\uff1acontig\u9700\u2265\u53c2\u8003\u5e8f\u5217\u957f\u5ea6\u7684\u767e\u5206\u6bd4\uff0c\u9ed8\u8ba40.75\u3002<br \/>&#8211;depth_multiplier\uff1a\u4e3b\u65c1\u7cfb\u540c\u6e90\u8986\u76d6\u5ea6\u9700\u2265\u5176\u4ed6\u65c1\u7cfb\u7684\u500d\u6570\uff0c\u9ed8\u8ba410\u3002<br \/>&#8211;chimeric_stitched_contig_check\uff1a\u68c0\u6d4b\u62fc\u63a5contig\u662f\u5426\u4e3a\u5d4c\u5408\u4f53\uff08\u9ed8\u8ba4\u5173\u95ed\uff09\u3002<br \/>&#8211;bbmap_subfilter\uff1a\u5141\u8bb8\u7684\u6700\u5927\u9519\u914d\u6570\uff0c\u9ed8\u8ba47\u3002<br \/>&#8211;trim_hit_sliding_window_size\uff1a\u6ed1\u52a8\u7a97\u53e3\u5927\u5c0f\uff0cExonerate\u9ed8\u8ba45\uff0cBLASTn\u9ed8\u8ba415\u3002<br \/>&#8211;trim_hit_sliding_window_thresh\uff1a\u7a97\u53e3\u76f8\u4f3c\u5ea6\u9608\u503c\uff0cExonerate\u9ed8\u8ba475%\uff0cBLASTn\u9ed8\u8ba465%\u3002<\/p><p><strong>\u901a\u7528\u6d41\u7a0b\u9009\u9879<\/strong><br \/>&#8211;start_from\/&#8211;end_with\uff1a\u6307\u5b9a\u6d41\u7a0b\u7684\u8d77\u59cb\u548c\u7ec8\u6b62\u6b65\u9aa4\uff0c\u4f8b\u5982&#8211;start_from assemble_reads\u3002<br \/>&#8211;force_overwrite\uff1a\u5f3a\u5236\u8986\u76d6\u5df2\u6709\u7ed3\u679c\u6587\u4ef6\uff08\u614e\u7528\uff09\u3002<br \/>&#8211;cpu\uff1a\u9650\u5236\u4f7f\u7528\u7684CPU\u6838\u5fc3\u6570\uff08\u9ed8\u8ba4\uff1a\u603b\u6838\u5fc3\u6570-1\uff09\u3002<br \/>&#8211;keep_intermediate_files\uff1a\u4fdd\u7559\u4e2d\u95f4\u6587\u4ef6\uff08\u9ed8\u8ba4\u5220\u9664\uff09\uff0c\u7528\u4e8e\u8c03\u8bd5\u3002<br \/>&#8211;verbose_logging\uff1a\u542f\u7528\u8be6\u7ec6\u65e5\u5fd7\uff08\u65e5\u5fd7\u4f53\u79ef\u53ef\u80fd\u589e\u592710\u500d\uff09\u3002<br \/>&#8211;hybpiper_output\uff1a\u6307\u5b9a\u8f93\u51fa\u76ee\u5f55\uff0c\u9ed8\u8ba4\u751f\u6210\u6837\u672c\u540d\u6587\u4ef6\u5939\u3002<\/p><p>###<\/p><p>\u00a0<\/p><p><span style=\"color: #ff0000;\"><strong>\u8f93\u51fa\u7ed3\u679c<\/strong><\/span><\/p><p>\uff081\uff09\u4ee5\u6837\u672c\u540d\u547d\u540d\u7684\u8f93\u51fa\u6587\u4ef6\u5939\uff0c\u4f8b\u5982\u6837\u672c\u540d\u5982\u679c\u4e3aSampleNale\uff0c\u90a3\u4e48\u6700\u540e\u6062\u590d\u7684\u5e8f\u5217\u4f4d\u4e8e\uff0cSampleName\/GeneName\/SampleName\/sequences\uff0c\u7ec4\u88c5\u7684\u5e8f\u5217\u5c31\u5728FAA\uff08\u86cb\u767d\uff09\u548cFNA\uff08cds\uff09\u6587\u4ef6\u5939\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-4a6b1d7 elementor-widget elementor-widget-text-editor\" data-id=\"4a6b1d7\" 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>\u63a5\u4e0b\u6765\u8fd0\u884cstats\u6a21\u5757<\/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-ee42c2b elementor-widget elementor-widget-text-editor\" data-id=\"ee42c2b\" 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>\u51c6\u5907\u4e00\u4e2aSample.txt\u6587\u4ef6\uff0c\u50a8\u5b58\u4e86\u6837\u672c\u7684\u540d\u5b57\uff0c\u6bcf\u884c\u4e00\u4e2a\u6837\u672c\u3002\u4f8b\u5982\uff0c<\/p><p>Sample1<\/p><p>Sample2<\/p><p>Sample3<\/p><p>\u00a0<\/p><p># \u8fd0\u884c<\/p><p>hybpiper stats -t_dna ref_allgenes.fasta gene namelist.txt<\/p><p>\u00a0<\/p><p>###\u00a0<\/p><p>-t \u76ee\u6807\u57fa\u56e0\u6587\u4ef6<\/p><p>###<\/p><p>\u00a0<\/p><p><span style=\"color: #ff0000;\"><strong>\u8f93\u51fa\u7ed3\u679c<\/strong><\/span><\/p><p>\uff081\uff09seq_lengths.tsv \uff1a\u540e\u7eed\u7ed8\u5236\u57fa\u56e0\u7684\u6062\u590d\u60c5\u51b5\u70ed\u56fe\u9700\u8981\u7684\u6587\u4ef6<\/p><p>\uff082\uff09hybpiper_stats.tsv\uff1a\u4f5c\u7528\u672a\u77e5\uff0c\u611f\u89c9\u6ca1\u4ec0\u4e48\u7528<\/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-3f7899d elementor-widget elementor-widget-text-editor\" data-id=\"3f7899d\" 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>\u8fd0\u884crecovery_heatma\u53ef\u89c6\u5316\u57fa\u56e0\u6062\u590d\u60c5\u51b5<\/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-23ed68b elementor-widget elementor-widget-text-editor\" data-id=\"23ed68b\" 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>hybpiper recovery_heatmap seq_lengths.tsv<\/p><p>\u00a0<\/p><p><span style=\"color: #ff0000;\">\u53ef\u80fd\u6709\u7528\u7684\u53c2\u6570<\/span><\/p><p>###<\/p><p>&#8211;figure_length\uff1a\u8f93\u51fa\u7684\u56fe\u7247\u957f\u5ea6\uff0c\u5982\u679c\u6062\u590d\u7684\u57fa\u56e0\u6570\u91cf\u5f88\u591a\uff0c\u53ef\u4ee5\u901a\u8fc7\u8fd9\u4e2a\u53c2\u6570\u6765\u964d\u4f4e\u9ad8\u5ea6\uff0c\u4ece\u800c\u7f29\u77ed\u6bcf\u4e2a\u70ed\u56fe\u5757\u7684\u957f\u5ea6\uff0c\u8ba9\u56fe\u770b\u8d77\u6765\u8212\u670d\u4e00\u4e9b<br \/>&#8211;figure_height\uff1a\u8f93\u51fa\u7684\u56fe\u7247\u9ad8\u5ea6<\/p><p>&#8211;no_xlabels \u4e0d\u663e\u793ax\u8f74\u6807\u7b7e\uff0c\u5f88\u6709\u7528\uff0c\u5982\u679c\u57fa\u56e0\u6570\u679c\u51bb\uff0c\u7f29\u77ed\u4e86\u957f\u5ea6\u4f1a\u8ba9\u6240\u6709\u57fa\u56e0\u7684ID\u6324\u5728\u4e00\u8d77<br \/>&#8211;no_ylabels \u4e0d\u663e\u793ay\u8f74\u6807\u7b7e<\/p><p>###<\/p><p><span style=\"color: #ff0000;\">\u8f93\u51fa\u7ed3\u679c<\/span><\/p><p>recovery_heatmap.png\uff1a\u57fa\u56e0\u6062\u590d\u60c5\u51b5\u70ed\u56fe<\/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-fec3226 elementor-widget elementor-widget-text-editor\" data-id=\"fec3226\" 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>\u8fd0\u884cparalog_retriever\u6536\u96c6\u6bcf\u4e2a\u57fa\u56e0\u7684\u5047\u5b9a\u7684\u65c1\u7cfb\u540c\u6e90\u57fa\u56e0<\/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-56c1e93 elementor-widget elementor-widget-code-highlight\" data-id=\"56c1e93\" 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>hybpiper paralog_retriever -t_dna ..\/Chr_6.fasta --fasta_dir_all paralogs_all --fasta_dir_no_chimeras paralogs_no_chimeras  --paralogs_list_threshold_percentage 0 --heatmap_filename paralog_heatmap Sample.txt --figure_length 10 --no_xlabels<\/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-e06df65 elementor-widget elementor-widget-text-editor\" data-id=\"e06df65\" 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>\u8fd0\u884c\u8fd9\u4e00\u6b65\u540e\uff0c\u4f1a\u5c31\u5728\u8f93\u51fa\u6587\u4ef6\u4e2d\u5f97\u5230\u6bcf\u4e2a\u57fa\u56e0\u7684\u6bcf\u4e2a\u7269\u79cd\u7ec4\u88c5\u51fa\u6765\u7684\u6bcf\u4e2a\u57fa\u56e0\uff0c\u5305\u62ec\u76f4\u7cfb\u548c\u5047\u5b9a\u7684\u65c1\u7cfb\uff0c\u63a5\u4e0b\u6765\u4f7f\u7528Pagone-nf\u53bb\u9664\u65c1\u7cfb\u540c\u6e90\u57fa\u56e0<\/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-c39b22b elementor-widget elementor-widget-code-highlight\" data-id=\"c39b22b\" 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>nextflow run ~\/Software\/paragone-nf\/paragone-nf\/paragone.nf -c ~\/Software\/paragone-nf\/paragone-nf\/paragone.config -profile standard_singularity --gene_fasta_directory  paralogs_all --external_outgroups_file ..\/Chr_6.fasta --external_outgroups Artemisia_annua,Chrysanthemum_rhombifolium --mo --mi --rt --threads 10 --outdir paragone_result\n\n# --external_outgroups_file \u6307\u5b9a\u5916\u7c7b\u7fa4\u5e8f\u5217\u6587\u4ef6 \n# -external_outgroups \u6307\u5b9a\u5916\u7c7b\u7fa4\u7269\u79cd <\/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-65546a0 elementor-widget elementor-widget-text-editor\" data-id=\"65546a0\" 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>\u6700\u540e\u7684\u8f93\u51fa\u7ed3\u679c\u662f\u4e00\u4e2a\u6587\u4ef6\u5939\uff0c\u5176\u4e2d23 24 25 \u662f\u540e\u7eed\u5206\u6790\u8981\u7528\u5230\u7684\u6570\u636e\u96c6<\/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-b57aa08 elementor-widget elementor-widget-image\" data-id=\"b57aa08\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"935\" height=\"691\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/03\/\u5fae\u4fe1\u56fe\u7247_20250609213231.png\" class=\"attachment-large size-large wp-image-1606\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/03\/\u5fae\u4fe1\u56fe\u7247_20250609213231.png 935w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/03\/\u5fae\u4fe1\u56fe\u7247_20250609213231-300x222.png 300w, 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