{"id":2066,"date":"2025-09-16T10:47:06","date_gmt":"2025-09-16T02:47:06","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2066"},"modified":"2025-12-23T17:47:05","modified_gmt":"2025-12-23T09:47:05","slug":"%e8%ae%b0%e5%bd%95%e4%b8%80%e6%ac%a1%e5%a4%9a%e5%80%8d%e4%bd%93%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%bb%84%e7%bb%84%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/09\/16\/%e8%ae%b0%e5%bd%95%e4%b8%80%e6%ac%a1%e5%a4%9a%e5%80%8d%e4%bd%93%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%bb%84%e7%bb%84%e8%a3%85\/","title":{"rendered":"\u8bb0\u5f55\u4e00\u6b21\u591a\u500d\u4f53\u57fa\u56e0\u7ec4\u7ec4\u7ec4\u88c5"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"2066\" class=\"elementor elementor-2066\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-4fdc0a6 e-flex e-con-boxed e-con e-parent\" data-id=\"4fdc0a6\" data-element_type=\"container\" 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class=\"elementor-element elementor-element-de07f6c elementor-widget elementor-widget-text-editor\" data-id=\"de07f6c\" 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>\u65e2\u7136\u627e\u5230\u95ee\u9898\u4e86\uff0c\u63a5\u4e0b\u6765\u5c31\u662f\u89e3\u51b3\u4e86\uff0c\u66fe\u8001\u5e08\u63a8\u8350\u7684\u65b9\u6848\u662f\uff0c\u628acollapse\u533a\u57df\u7684contig\u76f4\u63a5\u590d\u5236\u4e00\u4e2a\u62f7\u8d1d\uff0c\u76f8\u5f53\u4e8e\u662f\u624b\u52a8\u7684\u5236\u9020\u4e00\u4e2a\u62f7\u8d1d\uff0c\u7136\u540e\u6302\u8f7d\u4e0a\u53bb\u3002\u8fd9\u4e2a\u65b9\u6848\u7684\u7b2c\u4e00\u6b65\u5c31\u662f\u8981\u786e\u5b9a\u90a3\u4e9b\u533a\u57df\u662fcollapse\u533a\u57df\uff0c\u53ef\u4ee5\u901a\u8fc7\u6ed1\u7a97\u7edf\u8ba1ont\u6d4b\u5e8f\u6df1\u5ea6\u6765\u770b\u90a3\u4e9b\u533a\u57df\u662fcollapse\u533a\u57df\u3002\u66fe\u8001\u5e08\u7684\u6587\u7ae0\u4e2d\u5f62\u8c61\u751f\u52a8\u7684\u89e3\u91ca\u4e86\u4ec0\u4e48\u662fcollapse<span style=\"color: #ff0000;\"><strong>\uff08\u6b64\u65b9\u6cd5\u884c\u4e0d\u901a\uff0c\u8bf7\u81ea\u884c\u770b\u4e0b\u9762\u7684\u52a0\u7b14\uff09<\/strong><\/span>\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-752afeb elementor-widget elementor-widget-image\" data-id=\"752afeb\" 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 decoding=\"async\" width=\"1024\" height=\"317\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/31923436b6856faddb2bc005b8381c59-1024x317.png\" class=\"attachment-large size-large wp-image-2071\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/31923436b6856faddb2bc005b8381c59-1024x317.png 1024w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/31923436b6856faddb2bc005b8381c59-300x93.png 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/31923436b6856faddb2bc005b8381c59-768x238.png 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/31923436b6856faddb2bc005b8381c59.png 1464w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t\t\t\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-c003afa elementor-widget elementor-widget-button\" data-id=\"c003afa\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"button.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-button-wrapper\">\n\t\t\t\t\t<a class=\"elementor-button elementor-button-link elementor-size-sm\" href=\"https:\/\/pan.baidu.com\/s\/1I1CYt3qgRY6yTODIa9vf4w?pwd=yd8n\" target=\"_blank\">\n\t\t\t\t\t\t<span class=\"elementor-button-content-wrapper\">\n\t\t\t\t\t\t\t\t\t<span class=\"elementor-button-text\">plot_depth_along_chromosome.py<\/span>\n\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/a>\n\t\t\t\t<\/div>\n\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-60ad514 elementor-widget elementor-widget-code-highlight\" data-id=\"60ad514\" 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>minimap2 -t 60 -ax map-ont out_JBAT.FINAL.fa ..\/..\/..\/YY-2.pass.all.fq.gz|samtools view -bS -@ 60 - | samtools sort -@ 60 -o aln.sorted.bam\nsamtools index aln.sorted.bam\nmosdepth -t 10 --by 100000 100000_genome_depth aln.sorted.bam\n# plot depth stat result\npython plot_depth_along_chromosome.py -i 100000_genome_depth.regions.bed -c scaffold_10 -o scaffold_10.png\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-483abd7 elementor-widget elementor-widget-image\" data-id=\"483abd7\" 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 decoding=\"async\" width=\"785\" height=\"1024\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/scaffold_13_\u5408\u5e76-785x1024.jpg\" class=\"attachment-large size-large wp-image-2103\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/scaffold_13_\u5408\u5e76-785x1024.jpg 785w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/scaffold_13_\u5408\u5e76-230x300.jpg 230w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/scaffold_13_\u5408\u5e76-768x1002.jpg 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/scaffold_13_\u5408\u5e76-1178x1536.jpg 1178w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/scaffold_13_\u5408\u5e76.jpg 1393w\" sizes=\"(max-width: 785px) 100vw, 785px\" \/>\t\t\t\t\t\t\t\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-1be5d69 elementor-widget elementor-widget-text-editor\" data-id=\"1be5d69\" 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>\u53ef\u4ee5\u770b\u5230\u6709\u4e00\u4e2a\u975e\u5e38\u660e\u663e\u7684collpase\u533a\u57df\uff0c\u6df1\u5ea6\u8d85\u8fc7\u4e8640\u3002\u8fd9\u4e9b\u533a\u57df\u53ef\u4ee5\u548cHIC\u70ed\u56fe\u4e0a\u7684collpase\u533a\u76f8\u4e92\u5bf9\u5e94\u3002\u63a5\u4e0b\u6765\u53ea\u8981\u627e\u5230\u8fd9\u4e9bcontig\u5c31\u53ef\u4ee5\u4e86\u3002Juicebox\u975e\u5e38\u597d\u7528\uff0c\u9009\u4e2dcollapse\u533a\u7684contig\u5c31\u53ef\u4ee5\u663e\u793a\u51fa\u8fd9\u4e9bcontig\u7684\u540d\u5b57\uff0c\u6574\u7406\u5230\u4e00\u4e2a\u6587\u4ef6\u540e\uff0c\u7136\u540e\u6839\u636eout_JBAT.liftover.agp\u8fd9\u4e2a\u6587\u4ef6\uff0c\u5c31\u53ef\u4ee5\u8f6c\u6362\u4e3a\u539f\u59cb\u7684contigID\u3002\u7136\u540e\u5728\u628a\u590d\u5236\u7684\u548c\u5176\u4ed6\u5408\u5e76\u5230\u4e00\u4e2a\u6587\u4ef6\uff0c\u91cd\u65b0\u6302\u8f7d\u5c31\u53ef\u4ee5\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-f6860a2 elementor-widget elementor-widget-code-highlight\" data-id=\"f6860a2\" 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>grep -f Copy_contig.txt out_JBAT.liftover.agp > Copy_contig_id.txt\nseqkit grep -f Copy_contig_id.txt > Copy_contig.fasta\ncat ..\/..\/out_JBAT.FINAL.fa Copy_contig.fasta > Addcopy_out_JBAT.FINAL.fa\nbwa mem -5SP -t 30 Add_copy_out_JBAT.FINAL.fa ..\/..\/..\/..\/..\/..\/Hi-C\/NY-1_1.fq.gz ..\/..\/..\/..\/..\/..\/Hi-C\/NY-1_2.fq.gz  | samblaster | samtools view - -@ 30 -S -h -b -F 3340 -o Add_copy_out_JBAT.FINAL.bam\n~\/Software\/HapHiC\/utils\/filter_bam Add_copy_out_JBAT.FINAL.bam 1 --nm 3 --threads 50 | samtools view - -b -@ 50 -o  Add_copy_out_JBAT.FINAL_filtered.bam\n~\/Software\/HapHiC\/haphic pipeline Add_copy_out_JBAT.FINAL.fa .\/Add_copy_out_JBAT.FINAL_filtered.bam 60 --correct_nrounds 2 --threads 40 --processes 40 --outdir Add_copy_out_JBAT.FINAL_filter<\/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-a401d79 elementor-widget elementor-widget-heading\" data-id=\"a401d79\" 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. 20251016\u52a0\u7b14<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c13b67d elementor-widget elementor-widget-text-editor\" data-id=\"c13b67d\" 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>\u8ddd\u79bb\u4e0a\u6b21\u66f4\u65b0\u8fd9\u7bc7\u535a\u5ba2\u5df2\u7ecf\u8fc7\u53bb\u4e00\u4e2a\u591a\u6708\u4e86\uff0c\u4e0a\u6b21\u7684\u7b56\u7565\u662f\u884c\u4e0d\u901a\u7684\u3002\u539f\u56e0\u662f\u590d\u5236\u4e86\u574d\u584c\u533a\u7684\u5e8f\u5217\u540e\uff0cHIC\u6570\u636e\u6bd4\u5bf9\u7684\u65f6\u5019\uff0c\u4f1a\u51fa\u73b0\u91cd\u590d\u6bd4\u5bf9\uff0c\u5728\u540e\u7eed\u8fc7\u6ee4\u7684\u65f6\u5019\u4f1a\u88ab\u76f4\u63a5\u8fc7\u6ee4\u6389\uff0c\u5bfc\u81f4\u574d\u584c\u533a\u5b8c\u5168\u6ca1\u6709\u6bd4\u5bf9\uff0c\u56e0\u6b64\u6ca1\u6709\u4fe1\u53f7\u3002\u6b63\u786e\u7684\u601d\u8def\u662f\u4f7f\u7528C-pasing\u8fd9\u4e2a\u8f6f\u4ef6\u4e2d\u7684Collapse\u529f\u80fd\uff0c\u5bf9\u590d\u5236\u574d\u584c\u533a\u540e\u5bf9\u574d\u584c\u533a\u7684hic\u4fe1\u53f7\u8fdb\u884c\u968f\u673a\u5206\u914d\uff0c\u786e\u4fdd\u574d\u584c\u533a\u6709\u4fe1\u53f7\u3002\u8f6f\u4ef6\u7684\u4f5c\u8005\u4e3b\u8981\u662f\u901a\u8fc72\u79cd\u65b9\u6cd5\u6765\u8bc6\u522b\u574d\u584c\u533a\uff0c\u5206\u522b\u662fhifiasm\u7684gfa\u6587\u4ef6\u548cMapping\u7684depth\uff0c\u4f46\u662f\u6211\u6d4b\u8bd5\u4e0b\u6765\uff0c\u4f5c\u8005\u5b98\u7f51\u7684\u6d41\u7a0b\u53ea\u80fd\u5e94\u5bf92\u6761\u67d3\u8272\u4f53\u4e4b\u95f4\u7684\u574d\u584c\u533a\uff0c\u5982\u679c\u67d0\u4e00\u574d\u584c\u533a\uff0c\u5b58\u57283\u4e2a\u53ca3\u4e09\u4e2a\u4ee5\u4e0a\u67d3\u8272\u4f53\u7684\u574d\u584c\uff0c\u65e0\u6cd5\u51fa\u6765\u3002\u7ecf\u8fc7\u672c\u4eba\u7684\u4e0d\u61c8\u52aa\u529b\uff0c\u7ec8\u4e8e\u89e3\u51b3\u4e86\u8fd9\u4e2a\u95ee\u9898\u3002\u56e0\u6b64\u4e0b\u9762\u7684\u6559\u7a0b\u5206\u4e3a\u4e24\u4e2a\u677f\u5757\uff081\uff09\u4e24\u4e2a\u67d3\u8272\u4f53\u7684\u574d\u584c\u533a\u7684\u5904\u7406\uff082\uff09\u4e09\u4e2a\u53ca\u4ee5\u4e0a\u67d3\u8272\u4f53\u574d\u584c\u533a\u7684\u5904\u7406<\/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-f6cb6c3 elementor-widget elementor-widget-heading\" data-id=\"f6cb6c3\" 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\">2.1 \u4e24\u4e2a\u67d3\u8272\u4f53\u574d\u584c\u533a<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c45670e elementor-widget elementor-widget-text-editor\" data-id=\"c45670e\" 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>\u4e24\u4e2a\u67d3\u8272\u4f53\u4e4b\u95f4\u7684\u574d\u584c\u533a\u76f8\u5bf9\u7b80\u5355\uff0c\u8bc6\u522b\u5230\u574d\u584c\u533a\u540e\uff0c\u76f4\u63a5\u628a\u574d\u584c\u7684contig\u590d\u5236\uff0c\u7136\u540e\u5206\u914dclutster\uff0c\u91cd\u547d\u540d\uff0c\u91cd\u65b0\u6302\u8f7d\u5206\u914d\u4fe1\u53f7\u5c31\u53ef\u4ee5\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-ae192fa elementor-widget elementor-widget-code-highlight\" data-id=\"ae192fa\" 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># C-phasing\u6302\u8f7d\ncphasing pipeline -f hap_n_12.hic.p_utg.fa -hic1 ..\/..\/..\/..\/Hi-C\/NY-1_1.fq.gz -hic2 ..\/..\/..\/..\/Hi-C\/NY-1_2.fq.gz -t 40 -n 8:8\n\n# -hic1 -hic2 \u53cc\u7aef\u7684\u6d4b\u5e8f\u6587\u4ef6\n# -n 8:8 \u8fd9\u4e2a\u6307\u7684\u662f\u201c\u500d\u6027\uff1a\u67d3\u8272\u4f53\u6570\u91cf\u201d\uff0c\u4f8b\u5982\uff0c16\u500d\u4f53\uff0c\u500d\u6027\u4e3a8\uff0c\u90a3\u4e48\u4e00\u4e2a\u5355\u500d\u578b\u5c31\u662f8\uff1a8\n\n# \u57fa\u4e8eHifiasm\u751f\u6210\u7684gfa\u6587\u4ef6\u8bc6\u522b\u574d\u584c\u533a\ncphasing collapse from-gfa ..\/hap_n_12.hic.p_utg.noseq.gfa\n\n# \u751f\u6210\u4e00\u4e2acontigs.collapsed.contig.list\uff0c\u8fd9\u662f\u584c\u9677\u7684contig\n\n# \u5c06\u574d\u584c\u7684contig\u8fdb\u884c\u5206\u914d\u5230\u76f8\u5e94\u7684clusters\uff08\u67d3\u8272\u4f53\uff09\nphasing collapse rescue 3.hyperpartition\/NY-1.pairs.q1.e5m.hg hap_n_12.hic.p_utg.contigsizes 3.hyperpartition\/output.clusters.txt contigs.collapsed.contig.list -n 4 -at 3.hyperpartition\/hap_n_12.hic.p_utg.allele.table\n\n# \u751f\u6210\u4e00\u4e2acollapsed.rescue.clusters.txt\u548ccollapsed.rescue.contigs.list\uff0c\u8bb0\u5f55\u574d\u584ccontig\u7684\u5206\u914d\u548c\u91cd\u547d\u540d\u7684\u89c4\u5219\n\n# \u91cd\u65b0\u8fd0\u884cScaffolding\ncphasing scaffolding collapsed.rescue.clusters.txt  .\/2.prepare\/NY-1.counts_AAGCTT.txt \\\n     .\/2.prepare\/NY-1.clm.gz   \\\n     -at .\/3.hyperpartition\/hap_n_12.hic.p_utg.allele.table \\\n     -sc .\/2.prepare\/NY-1.split.contacts \\\n     -f ..\/hap_n_12.hic.p_utg.fa \\\n     -t 40 \\\n     -o groups.agp \\\n     -m precision\n\n# \u751f\u6210\u4e00\u4e2a\u65b0\u7684agp\u6587\u4ef6\uff0c\u8fd9\u65f6\u65b0\u590d\u5236\u7684\u574d\u584ccontig\u5df2\u7ecf\u6302\u5728\u6210\u529f\u5e76\u4e14\u5206\u914d\u5230\u4e86\u4fe1\u53f7,\u4f46\u662f\u65b0\u590d\u5236\u7684contig ID\u548c\u4e4b\u524d\u7684\u662f\u91cd\u590d\u7684\n\n# \u751f\u6210\u4e00\u4e2a\u65b0\u7684contig\u6c34\u5e73\u7684fasta\u548cagp\u6587\u4ef6\uff0c\u4e3b\u8981\u76ee\u7684\u662f\u91cd\u547d\u540d\u590d\u5236\u7684contig\ncphasing agp2fasta  groups.agp ..\/hap_n_12.hic.p_utg.fa --contigs > draft.dup.fasta\ncphasing collapse agp-dup groups.agp > groups.dup.agp\n\n# \u751f\u6210\u65b0\u7684pairs.pqs\u6587\u4ef6\ncphasing collapse pairs-dup NY-1.pairs.pqs collapsed.rescue.contigs.list -o sample.dup.pairs.pqs\n\n# \u751f\u6210Juicebox\u7684\u8f93\u5165\u6587\u4ef6.assmbly\ncphasing utils agp2assembly groups.dup.agp > groups.dup.assembly\ncphasing pairs2mnd sample.dup.pairs.pqs -o sample.dup.mnd.txt\n\n# \u751f\u6210Juicebox\u7684\u8f93\u5165\u6587\u4ef6.hic\uff0c\u6ce8\u610f\uff0c\u8fd9\u4e00\u6b65\u9700\u8981\u7528\u52303d-dna\uff0c\u8bf7\u81ea\u884c\u4e0b\u8f7d\uff0c\u5e76\u627e\u5230run-assembly-visualizer.sh\u6587\u4ef6\nbash ~\/Software\/3d-dna\/visualize\/run-assembly-visualizer.sh groups.dup.assembly sample.dup.mnd.txt\n\n# \u751f\u6210\u65b0\u7684corrected.pairs.gz\uff08\u53ef\u9009\u6b65\u9aa4\uff0c\u53ea\u6709\u5bf9contig\u8fdb\u884c\u5207\u5272\u540e\u624d\u9700\u8981\uff09\ncphasing-rs pairs-break sample.dup.pairs.pqs break.bed\n\n# \u57fa\u4e8e\u8c03\u6574\u7684groups.review.assembly\u751f\u6210\u6700\u7ec8\u7684agp\u6587\u4ef6\ncphasing utils assembly2agp groups.dup.review.assembly -n 8:8\n\n# \u8fd9\u4e00\u6b65\u4f1a\u751f\u6210groups.dup.review.agp\u548cgroups.dup.review.corrected.agp\uff08\u53ea\u6709contig\u8fdb\u884c\u5207\u5272\u540e\u624d\u4f1a\u751f\u6210\uff0c\u5e76\u4e14\u540e\u7eed\u5206\u6790\u90fd\u8981\u4f7f\u7528\u8fd9\u4e2a\u6587\u4ef6\u66ff\u4ee3groups.dup.review.agp\uff09\n\n# \u751f\u6210\u6700\u540e\u7684\u57fa\u56e0\u7ec4\ncphasing agp2fasta groups.review.agp draft.asm.fasta > groups.review.asm.fasta\n\n# \u7ed8\u5236\u65b0\u7684\u70ed\u56fe\ncphasing pairs2cool sample.dup.pairs.pqs sample.dup.pairs.pqs\/_contigsizes sample.10k.cool \ncphasing plot -a groups.dup.review.agp -m sample.10k.cool -o sample.500k.wg.png<\/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-c391993 elementor-widget elementor-widget-heading\" data-id=\"c391993\" 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\">2.1 \u4e09\u4e2a\u53ca\u4e09\u4e2a\u4ee5\u4e0a\u67d3\u8272\u4f53\u574d\u584c\u533a<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-270dab2 elementor-widget elementor-widget-text-editor\" data-id=\"270dab2\" 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\u79cd\u60c5\u51b5\u4e0b\u76f8\u5bf9\u590d\u6742\uff0c\u4e3b\u8981\u95ee\u9898\u51fa\u5728\u751f\u6210\u201ccollapsed.rescue.clusters.txt\u201d\u6587\u4ef6\u7684\u6b65\u9aa4\uff0c\u56e0\u4e3a\u5b58\u5728\u574d\u584c\u533a\u5728\u91cd\u65b0\u5206\u914d\u7684\u65f6\u5019\uff0c\u51fa\u73b0\u4e86\u591a\u79cd\u60c5\u51b5\uff0c\u6240\u4ee5\u4f1a\u51fa\u73b0\u53ea\u5206\u914d\u5230\u4e09\u4e2a\u67d3\u8272\u4f53\u4e2d\u7684\u4e24\u4e2a\uff0c\u6216\u8005\u76f4\u63a5\u4e0d\u5206\u914d\u3002\u8fd9\u79cd\u60c5\u51b5\u4e0b\u89e3\u51b3\u65b9\u6cd5\u5176\u5b9e\u4e5f\u5f88\u7b80\u5355\uff0c\u5c31\u662f\u624b\u52a8\u4fee\u6539\u201ccollapsed.rescue.clusters.txt\u201d\u6587\u4ef6\uff0c\u5c06\u574d\u584c\u533a\u7684contiguous\u8fdb\u884c\u624b\u52a8\u7684\u5206\u914d\u3002\u968f\u540e\u624b\u52a8\u4fee\u6539\u201ccollapsed.rescue.contigs.list\u201d\u6587\u4ef6\uff0c\u7ed9\u574d\u584c\u533a\u7684contig\u8fdb\u884c\u591a\u6b21\u91cd\u547d\u540d\uff0c\u7136\u540e\u8854\u63a5\u4e0b\u6e38\u7684\u6d41\u7a0b\u5373\u53ef\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-518c023 elementor-widget elementor-widget-code-highlight\" data-id=\"518c023\" 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># C-phasing\u6302\u8f7d\ncphasing pipeline -f hap_n_12.hic.p_utg.fa -hic1 ..\/..\/..\/..\/Hi-C\/NY-1_1.fq.gz -hic2 ..\/..\/..\/..\/Hi-C\/NY-1_2.fq.gz -t 40 -n 8:8\n\n# -hic1 -hic2 \u53cc\u7aef\u7684\u6d4b\u5e8f\u6587\u4ef6\n# -n 8:8 \u8fd9\u4e2a\u6307\u7684\u662f\u201c\u500d\u6027\uff1a\u67d3\u8272\u4f53\u6570\u91cf\u201d\uff0c\u4f8b\u5982\uff0c16\u500d\u4f53\uff0c\u500d\u6027\u4e3a8\uff0c\u90a3\u4e48\u4e00\u4e2a\u5355\u500d\u578b\u5c31\u662f8\uff1a8\n\n# \u57fa\u4e8eHifiasm\u751f\u6210\u7684gfa\u6587\u4ef6\u8bc6\u522b\u574d\u584c\u533a\ncphasing collapse from-gfa ..\/hap_n_12.hic.p_utg.noseq.gfa\n\n# \u751f\u6210\u4e00\u4e2acontigs.collapsed.contig.list\uff0c\u8fd9\u662f\u584c\u9677\u7684contig\n\n# \u5c06\u574d\u584c\u7684contig\u8fdb\u884c\u5206\u914d\u5230\u76f8\u5e94\u7684clusters\uff08\u67d3\u8272\u4f53\uff09\nphasing collapse rescue 3.hyperpartition\/NY-1.pairs.q1.e5m.hg hap_n_12.hic.p_utg.contigsizes 3.hyperpartition\/output.clusters.txt contigs.collapsed.contig.list -n 4 -at 3.hyperpartition\/hap_n_12.hic.p_utg.allele.table\n\n# \u751f\u6210\u4e00\u4e2acollapsed.rescue.clusters.txt\u548ccollapsed.rescue.contigs.list\uff0c\u8bb0\u5f55\u574d\u584ccontig\u7684\u5206\u914d\u548c\u91cd\u547d\u540d\u7684\u89c4\u5219\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-9fd3495 elementor-widget elementor-widget-text-editor\" data-id=\"9fd3495\" 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\uff0c\u624b\u52a8\u4fee\u6539\u201ccollapsed.rescue.clusters.txt\u201d\u5206\u914d\u574d\u584c\u533a\u7684contig<\/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-ef1947f elementor-widget elementor-widget-image\" data-id=\"ef1947f\" 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 loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"490\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_225617_060-1024x490.png\" class=\"attachment-large size-large wp-image-2187\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_225617_060-1024x490.png 1024w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_225617_060-300x144.png 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_225617_060-768x368.png 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_225617_060-1536x735.png 1536w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_225617_060.png 1905w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t\t\t\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-68df6aa elementor-widget elementor-widget-text-editor\" data-id=\"68df6aa\" 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>\u5982\u56fe\u6240\u793a\uff0c\u84dd\u8272\u6846\u4ee3\u8868\u7684\u662f\u76f4\u63a5\u5206\u914d\u540e\u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u770b\u5230Chr06g7\u548cChr06g8\u6ca1\u6709\u5f97\u5230\u4efb\u4f55\u5206\u914d\uff0c\u56e0\u6b64\u8981\u624b\u52a8\u8fdb\u884c\u5206\u914d\u3002\u4f46\u662f\u600e\u4e48\u77e5\u9053\u8fd9\u4e9b\u574d\u584c\u533a\u6709\u90a3\u4e9bcontig\u5462\uff1f\u5176\u5b9e\u5f88\u7b80\u5355\uff0c\u76f4\u63a5\u628a\u521d\u59cb\u7684\u6302\u8f7d\u7ed3\u679c\u5bfc\u5165\u8fdbjuicebox\uff0c\u9009\u4e2d\u574d\u584c\u533a\uff0c\u5c31\u80fd\u770b\u5230\u4e86\u3002\u7136\u540e\u628a\u8fd9\u4e9bcontig\uff0c\u5206\u522b\u6dfb\u52a0\u5230Chr06g7\u548cChr06g8\u4e2d\uff0c\u5c31\u53ef\u4ee5\u4e86\u3002\u9ec4\u8272\u6846\u4e3a\u6dfb\u52a0\u5230\u4e86\u5176\u4e2d\u4e00\u4e2a\u67d3\u8272\u4f53\uff0c\u7ea2\u8272\u6846\u4e3a\u4e24\u4e2a\u90fd\u6dfb\u52a0\u3002\u8fd9\u4e00\u6b65\u4e4b\u540e\uff0c\u6211\u4eec\u8fd8\u8981\u624b\u52a8\u4fee\u6539\u201ccollapsed.rescue.contigs.list\u201d\u6587\u4ef6\uff0c\u5bf9\u574d\u584c\u533a\u4e2d\u7684contig\u8fdb\u884c\u624b\u52a8\u7684\u91cd\u547d\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-db1ce06 elementor-widget elementor-widget-image\" data-id=\"db1ce06\" 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 loading=\"lazy\" decoding=\"async\" width=\"305\" height=\"393\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_230328_818.png\" class=\"attachment-large size-large wp-image-2192\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_230328_818.png 305w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u5fae\u4fe1\u56fe\u7247_2025-10-16_230328_818-233x300.png 233w\" sizes=\"(max-width: 305px) 100vw, 305px\" \/>\t\t\t\t\t\t\t\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-d3b0743 elementor-widget elementor-widget-text-editor\" data-id=\"d3b0743\" 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>\u8f6f\u4ef6\u7684\u9ed8\u8ba4\u547d\u540d\u89c4\u5219\u4e3a\u201c\u539f\u59cb\u7684contigid_d2\u201d\uff0c\u90a3\u4e48\u5982\u679c\u5982\u679c\u6709\u591a\u4e2a\u62f7\u8d1d\uff0c\u5c31\u662f_d3\uff0c_d4\u9010\u6e10\u589e\u52a0\u3002\u56e0\u6b64\uff0c\u624b\u52a8\u6539\u6210d_3\u3002\u8fd9\u6837\u6211\u4eec\u5c31\u62ff\u5230\u4e86\u6b63\u786e\u5206\u914dcontig\u7684collapsed.rescue.clusters.txt\u548ccollapsed.rescue.contig.list\uff0c\u8854\u63a5\u4e0b\u9762\u7684\u6b65\u9aa4\u5373\u53ef\u3002\u56e0\u4e3a\u540e\u7eed\u548c\u4e24\u6761\u67d3\u8272\u4f53\u7684\u4e0b\u6e38\u76f8\u540c\uff0c\u5c31\u4e0d\u5199\u4e86\uff0c\u53c2\u8003\u4e0a\u9762\u7684\u5373\u53ef\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-fe3ab36 elementor-widget elementor-widget-image\" data-id=\"fe3ab36\" 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 loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"444\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u672a\u6807\u9898-1-1024x444.png\" class=\"attachment-large size-large wp-image-2209\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u672a\u6807\u9898-1-1024x444.png 1024w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u672a\u6807\u9898-1-300x130.png 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u672a\u6807\u9898-1-768x333.png 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u672a\u6807\u9898-1-1536x666.png 1536w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/09\/\u672a\u6807\u9898-1-2048x887.png 2048w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t\t\t\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-f70d4b7 elementor-widget elementor-widget-text-editor\" data-id=\"f70d4b7\" 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>\u5de6\u8fb9\u662f\u672a\u5904\u7406\u574d\u584c\u533a\u7684hic\u70ed\u56fe\uff0c\u53f3\u8fb9\u662f\u5904\u7406\u540e\u7684\uff0c\u53ef\u4ee5\u770b\u5230\uff0c\u574d\u584c\u533a\u660e\u663e\u88ab\u5206\u6210\u4e86\u591a\u4e2a\uff0c\u5e76\u4e14\u5904\u7406\u524d\u7684\u57fa\u56e0\u7ec4\u5927\u5c0f\u4e3a1719.4\uff0c\u5904\u7406\u540e\u4e3a1801.9\uff0c\u8bf4\u660e\u574d\u584c\u533a\u7684\u6210\u529f\u590d\u5236\uff0c\u5bfc\u81f4\u57fa\u56e0\u7ec4\u53d8\u5927\u4e86\u3002<\/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>0. \u524d\u8a00 \u53bb\u5e74\u7684\u65f6\u5019\uff0c\u6211\u4eec\u7ec4\u60f3\u5728\u77ed\u65f6\u95f4\u5185\u5feb\u901f\u7684\u51fa\u4e00\u7bc7\u4e00\u533a\u7684\u6587\u7ae0\uff0c\u5728\u6211\u7684\u63a8\u8350\u4e0b\uff0c\u8001\u5e08\u9009\u62e9\u4e86\u90a3\u65f6\u5019\u8fd8\u5728\u98ce\u53e3\u6d6a\u5c16\u7684 &#8230; <a title=\"\u8bb0\u5f55\u4e00\u6b21\u591a\u500d\u4f53\u57fa\u56e0\u7ec4\u7ec4\u7ec4\u88c5\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/09\/16\/%e8%ae%b0%e5%bd%95%e4%b8%80%e6%ac%a1%e5%a4%9a%e5%80%8d%e4%bd%93%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%bb%84%e7%bb%84%e8%a3%85\/\" aria-label=\"\u9605\u8bfb \u8bb0\u5f55\u4e00\u6b21\u591a\u500d\u4f53\u57fa\u56e0\u7ec4\u7ec4\u7ec4\u88c5\">\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-2066","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\u591a\u500d\u4f53\u57fa\u56e0\u7ec4\u7ec4\u7ec4\u88c5 - \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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