{"id":1526,"date":"2025-04-17T17:00:02","date_gmt":"2025-04-17T09:00:02","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1526"},"modified":"2025-04-17T17:06:39","modified_gmt":"2025-04-17T09:06:39","slug":"getorganelle-%e7%bb%84%e8%a3%85%e8%b4%a8%e4%bd%93%e5%9f%ba%e5%9b%a0%e7%bb%84","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/04\/17\/getorganelle-%e7%bb%84%e8%a3%85%e8%b4%a8%e4%bd%93%e5%9f%ba%e5%9b%a0%e7%bb%84\/","title":{"rendered":"Getorganelle \u7ec4\u88c5\u8d28\u4f53\u57fa\u56e0\u7ec4"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1526\" class=\"elementor elementor-1526\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-17a0e62 e-flex e-con-boxed e-con e-parent\" data-id=\"17a0e62\" 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-9db6cf2 elementor-widget elementor-widget-heading\" data-id=\"9db6cf2\" 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\">Getorganelle \u7ec4\u88c5\u8d28\u4f53\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-1e157bc elementor-widget elementor-widget-heading\" data-id=\"1e157bc\" 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\n<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1bb3a94 elementor-widget elementor-widget-text-editor\" data-id=\"1bb3a94\" 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>Getorganelle\u53ef\u4ee5\u7528\u6765\u7ec4\u88c5\u6240\u6709\u7684\u8d28\u4f53\u57fa\u56e0\u7ec4\uff0c\u4f46\u662f\u6bd4\u8f83\u5e38\u7528\u662f\u7528\u6765\u7ec4\u88c5\u690d\u7269\u7684\u53f6\u7eff\u4f53\u57fa\u56e0\u7ec4\u3002\u4f46\u662f\u672c\u4eba\u5251\u8d70\u504f\u950b\u51b3\u5b9a\u7528\u5b83\u6765\u7ec4\u88c5\u771f\u83cc\u7684\u7ebf\u7c92\u4f53\u57fa\u56e0\u7ec4\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-82817b2 elementor-widget elementor-widget-heading\" data-id=\"82817b2\" 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-4e5edf6 elementor-widget elementor-widget-text-editor\" data-id=\"4e5edf6\" 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 Getorganelle<\/p><p>mamba activate Getorganelle<\/p><p>mamba install bioconda::getorganelle<\/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-a9d0646 elementor-widget elementor-widget-heading\" data-id=\"a9d0646\" 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. \u4e0b\u8f7d\u9700\u8981\u7684\u6570\u636e\u5e93<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1d4d57a elementor-widget elementor-widget-text-editor\" data-id=\"1d4d57a\" 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>get_organelle_config.py -a fungus_mt<\/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-6325024 elementor-widget elementor-widget-heading\" data-id=\"6325024\" 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\u884c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-e1be452 elementor-widget elementor-widget-text-editor\" data-id=\"e1be452\" 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># \u57fa\u4e8ereads\u8fdb\u884c\u7ec4\u88c5<br \/>get_organelle_from_reads.py -1 Unknown_CG553-001R0007_good_1.fq.gz -2 Unknown_CG553-001R0007_good_2.fq.gz -R 20 -k 21,45,65,85,105 -F fungus_mt -o Unknown_CG553-001R0007_s -t 50<\/p><p># -F \u6307\u5b9a\u7ec4\u88c5\u7684\u57fa\u56e0\u7ec4\u7c7b\u578b\uff0c\u6211\u6307\u5b9a\u7684\u662f\u771f\u83cc\u7684\u7ebf\u7c92\u4f53\u57fa\u56e0\u7ec4\uff0c\u6839\u636e\u81ea\u5df1\u7684\u9700\u6c42\u66f4\u6539<\/p><p># \u8f93\u51fa\u7ed3\u679c<\/p><p>\u5728\u6307\u5b9a\u7684\u8f93\u51fa\u6587\u4ef6\u5939\u4e2d\u4f1a\u6709\u7ec4\u88c5\u7684\u7ed3\u679c\uff0c\u4f1a\u51fa\u73b0\u4e09\u79cd\u60c5\u51b5<\/p><p>1. \u5b8c\u5168\u6210\u73af *complete*.fasta<\/p><p>2. \u63a5\u8fd1\u6210\u73af *nearly-complete*.fasta<\/p><p>3. \u6ca1\u6709\u6210\u73af *scaffolds*.fasta<\/p><p>\u4e00\u822c\u6765\u8bf4\uff0c\u53ea\u6709\u5b8c\u5168\u6210\u73af\u624d\u662f\u53ef\u4ee5\u7528\u7684\uff0c\u5982\u679c\u7ec4\u88c5\u4e0d\u6210\u6b22\uff0c\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u51e0\u4e2a\u65b9\u6cd5\u91cd\u65b0\u7ec4\u88c5\u53ef\u80fd\u4f1a\u6709\u6539\u5584\u3002<\/p><p>\uff081\uff09\u51cf\u5c0f-W \u53c2\u6570\u7684\u503c<\/p><p>\uff082\uff09-s \u53c2\u6570\u6dfb\u52a0\u53c2\u8003\u57fa\u56e0\u7ec4<\/p><p>\uff083\uff09\u589e\u52a0 -R \u53c2\u6570\uff0c\u589e\u52a0\u8fd0\u884c\u8f6e\u6570\u00a0<\/p><p>\uff084\uff09\u6dfb\u52a0&#8211;max-reads inf \u548c &#8211;reduce-reads-for-coverage\uff0c\u8fd9\u4e24\u4e2a\u53c2\u6570\u5c31\u662f\u589e\u52a0\u7ec4\u88c5\u4f7f\u7528\u7684reads\uff0c\u4f46\u662f\u4f1a\u589e\u52a0\u4f7f\u7528\u5185\u5b58\u548c\u65f6\u95f4<\/p><p>\u5982\u679c\u4e0a\u8ff0\u90fd\u6ca1\u6709\u6539\u5584\uff0c\u53ef\u4ee5\u5251\u8d70\u504f\u950b\u4f7f\u7528\u5176\u4ed6\u7684\u7ec4\u88c5\u7b56\u7565\u3002<\/p><p>\u00a0<\/p><p>1.\u00a0 \u751f\u6210Bowtie2+SPAdes\u7684\u7ec4\u88c5sh\u811a\u672c<\/p><p># \u751f\u6210\u8fd0\u884c\u811a\u672c<\/p><p>make_batch_for_iteratively_mapping_assembling.py -1 Unknown_CG553-001R0007_good_1.fq.gz -2 Unknown_CG553-001R0007_good_2.fq.gz -s Reference_07.fasta -R 10 -k 21,45,65,85,105 -o Unknown_CG553-001R0007_make_batch<\/p><p># \u8fd0\u884c\u811a\u672c<\/p><p>bash Unknown_CG553-001R0007_make_batch.sh<\/p><p>\u00a0<\/p><p>2. \u4f7f\u7528 join_spades_fastg_by_blast.py \u5728assembly_graph.fastg.extend-*.fastg \u6587\u4ef6 contigs \u4e4b\u95f4\u63d2\u5165\u95f4\u9699\uff0c\u7136\u540e\u4f7f\u7528 get_organelle_from_assembly.py \u4ece Graph A&#8217; \u4e2d\u63d0\u53d6\u5305\u542b\u95f4\u9699\u7684\u201c\u5b8c\u6574\u201d\u8d28\u7c92\u4f53\u57fa\u56e0\u7ec4\u3002<\/p><p># \u63d2\u5165\u95f4\u9699<\/p><p>join_spades_fastg_by_blast.py -g extended_K105.assembly_graph.fastg.extend-fungus_mt.fastg -f ..\/Reference_07.fasta<\/p><p># \u7ec4\u88c5<\/p><p>get_organelle_from_assembly.py -g .\/extended_K105.assembly_graph.fastg.extend-fungus_mt.fastg.Ncontigs_added.fastg -F fungus_mt -o output &#8211;min-depth 10<\/p><p>\u00a0<\/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>Getorganelle \u7ec4\u88c5\u8d28\u4f53\u57fa\u56e0\u7ec4 1. \u524d\u8a00 Getorganelle\u53ef\u4ee5\u7528\u6765\u7ec4\u88c5\u6240\u6709\u7684\u8d28\u4f53\u57fa\u56e0\u7ec4\uff0c\u4f46 &#8230; <a title=\"Getorganelle \u7ec4\u88c5\u8d28\u4f53\u57fa\u56e0\u7ec4\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/04\/17\/getorganelle-%e7%bb%84%e8%a3%85%e8%b4%a8%e4%bd%93%e5%9f%ba%e5%9b%a0%e7%bb%84\/\" aria-label=\"\u9605\u8bfb Getorganelle \u7ec4\u88c5\u8d28\u4f53\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":[1],"tags":[],"class_list":["post-1526","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Getorganelle \u7ec4\u88c5\u8d28\u4f53\u57fa\u56e0\u7ec4 - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, 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