{"id":70,"date":"2021-12-02T14:41:13","date_gmt":"2021-12-02T14:41:13","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/research-beta\/lees\/?page_id=70"},"modified":"2026-01-13T13:56:18","modified_gmt":"2026-01-13T13:56:18","slug":"software","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/research\/lees\/software\/","title":{"rendered":"Software"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\">\n<h3 class=\"wp-block-heading\">See <a href=\"https:\/\/www.bacpop.org\/software\/\">https:\/\/www.bacpop.org\/software\/<\/a> for a full list<\/h3>\n\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/github.com\/samhorsfield96\/ggCaller\" target=\"_blank\" rel=\"noreferrer noopener\">ggCaller<\/a><\/h3>\n\n\n\n<p>graph-gene Caller (<code>ggCaller<\/code>), combines gene annotation and pangenome clustering steps within population-wide de Bruijn Graphs.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/docs.rs\/ska\/latest\" data-type=\"URL\" data-id=\"https:\/\/docs.rs\/ska\/latest\" target=\"_blank\" rel=\"noreferrer noopener\">ska<\/a><\/h3>\n\n\n\n<p>Split k-mer analysis (<code>SKA<\/code>) can be used to produce alignments from closely related sequence assemblies or reads, quickly (because it is alignment-free) and with minimal fuss (due to the interface).<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/poppunk.net\/\" target=\"_blank\" rel=\"noreferrer noopener\">PopPUNK<\/a><\/h3>\n\n\n\n<p>Calculate core and accessory distances, cluster genomes, assign new genomes to clusters, make visualisations<br><\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><a href=\"https:\/\/github.com\/bacpop\/sketchlib.rust\" data-type=\"link\" data-id=\"https:\/\/github.com\/bacpop\/sketchlib.rust\">sketchlib.rust<\/a><\/h3>\n\n\n\n<p>A rust rewrite of pp-sketchlib particularly targeted at very large datasets by using a new file format. To find nearest neighbours or perform subset queries, this code is an improvement over pp-sketchlib.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"hahahugoshortcode21s14hbhb-menelmacar\"><a href=\"https:\/\/biomodels.bacpop.org\/\">Menelmacar<\/a><\/h3>\n\n\n\n<p>Making Execution of (Nearly) Every Life-science Model ACcessible to All Researchers<\/p>\n\n\n\n<p>Interactive visualisations of mathematical models from BioModels.<\/p>\n<\/div><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-70","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages\/70","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/comments?post=70"}],"version-history":[{"count":8,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages\/70\/revisions"}],"predecessor-version":[{"id":21985,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/pages\/70\/revisions\/21985"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/media?parent=70"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/lees\/wp-json\/wp\/v2\/embl_taxonomy?post=70"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}