{"id":3707,"date":"2016-07-04T16:20:56","date_gmt":"2016-07-04T14:20:56","guid":{"rendered":"https:\/\/www.toulouse-white-biotechnology.com\/insights\/actualites\/actualite\/the-bioinformatics-platform\/"},"modified":"2026-03-16T13:52:47","modified_gmt":"2026-03-16T12:52:47","slug":"the-bioinformatics-platform","status":"publish","type":"post","link":"https:\/\/www.toulouse-white-biotechnology.com\/en\/insights\/blog\/news\/the-bioinformatics-platform\/","title":{"rendered":"The bioinformatics platform"},"content":{"rendered":"<strong><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-5275 size-thumbnail\" src=\"https:\/\/www.toulouse-white-biotechnology.com\/app\/uploads\/2016\/07\/3-150x150-1.jpg\" alt=\"3\" width=\"150\" height=\"150\">This TWB platform operates in the context of the sequence data analysis<\/strong>\n\n<p>of TWB&#039;s R&amp;D projects.<\/p>\n\n<strong>The service offer of the TWB bioinformatics platform includes the de novo assembly of micro-organisms, re-sequencing and analysis of genomic variants and the differential expression analysis of genomes from RNAseq. TWB is also involved in metagenomics in order to identify certain enzymatic functions<\/strong>\n\n<p>. The data can be supplied by public databases or from sequencing services.<\/p>\n\n<strong>TWB relies on local sequencing platforms and enjoys a privileged environment in terms of second and third generation NGS (&#8220;Next Generation Sequencing&#8221;) technologies<\/strong>\n\n<p>. Indeed, the GeT network of platforms (genome and transcriptome<\/p>\n\n<a href=\"http:\/\/get.genotoul.fr\/index.php?id=216&amp;L=0&amp;tx_ttnews%5BbackPid%5D=18&amp;tx_ttnews%5Btt_news%5D=225)\" target=\"_blank\">http:\/\/get.genotoul.fr\/index.php?id=216&amp;L=0&amp;tx_ttnews[backPid]=18&amp;tx_ttnews[tt_news]=225)<\/a>\n\n<p>, possesses:<\/p>\n\n<ul class=\"wp-block-list\">\r\n\t<li>second generation sequencers:\r\n<ul>\r\n\t<li>Illumina HiSeq 2500 and 3000, MiSeq: &#8220;paired end&#8221; sequencing (sequencing of the two extremities of the fragments) with sizes ranging up to 300Pb<\/li>\r\n\t<li>Ion S5: up to 40 kb<\/li>\r\n<\/ul>\r\n<\/li>\r\n\t<li>third generation sequencers: PacBio RSII and MinION, producing long sequences.<\/li>\r\n<\/ul>\n\n<p>These platforms are in constant evolution, acquiring the latest technologies from year to year. They thus provide access to extensive local expertise and a network, in addition to access to all of the most advanced technical solutions for sequencing projects.<\/p>\n\n<figure class=\"wp-block-image\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-5276\" src=\"https:\/\/www.toulouse-white-biotechnology.com\/app\/uploads\/2016\/07\/4-1.jpg\" alt=\"4\" width=\"578\" height=\"433\"><\/figure>\n\n<p>[bloc_note]Legend: The ION S5 sequencer generates small chips with only 4 million sequences, thus allowing more flexible multiplex sequencing of isolated micro-organisms or 40 kb fosmids.[\/bloc_note]\r\n\r\nConcerning bioinformatic analyses,<\/p>\n\n<strong> the platform uses the local infrastructure of Bioinfo GenoToul for the power of calculation and disk space<\/strong>\n\n<p>(<\/p>\n\n<a href=\"http:\/\/bioinfo.genotoul.fr\/\" target=\"_blank\">http:\/\/bioinfo.genotoul.fr\/<\/a>\n\n<p>). This infrastructure also regularly develops this material, thus providing a comfortable bioinformatics working environment.<\/p>\n\n<strong>TWB is also committed to training users<\/strong>\n\n<p>in bioinformatic analysis in collaboration with SIGENAE (Information system of genomes and breeding animals) and the Bioinfo GenoToul platform, with the Galaxy software tool (<\/p>\n\n<a href=\"http:\/\/bioinfo.genotoul.fr\/index.php?id=10\" target=\"_blank\">http:\/\/bioinfo.genotoul.fr\/index.php?id=10<\/a>\n\n<p>). The local Galaxy entity allows the integration of customised tools (<\/p>\n\n<a href=\"https:\/\/galaxyproject.org\/\" target=\"_blank\">https:\/\/galaxyproject.org\/<\/a>\n\n<p>) and user-friendliness.\r\n\r\n[bloc_enavant]<\/p>\n\n<strong>TWB offers a complete package<\/strong>\n\n<p>from the outset of the project for matching\u00a0the different interlocutors (sequencing, bioinformatics analysis, biostatistics, training, etc.)\u00a0and enables the partners to quickly obtain information in response to their questions.[\/bloc_enavant]<\/p>\n\n<h2 class=\"wp-block-heading\">Examples of applications<\/h2>\n\n<ul class=\"wp-block-list\">\r\n\t<li><strong>Sequencing of strains of fungi, assemblage and annotation of genomes<\/strong><\/li>\r\n\t<li><strong>Analysis of the differential expression of the genes of 2 samples from 2 different conditions of culture of a plant<\/strong><\/li>\r\n\t<li><strong>Phylogenetic analysis of protein families (micro-organisms, plants)<\/strong>\r\n<strong> Training in Galaxy software<\/strong><\/li>\r\n<\/ul>\n\n<em>Contact: Sabrina Legoueix-Rodriguez, TWB Bioinformatics platform manager, (<a href=\"mailto:sabrina.rodriguez@toulouse.inra.fr\" target=\"_blank\">sabrina.rodriguez@toulouse.inra.fr<\/a>)<\/em>","protected":false},"excerpt":{"rendered":"<p>This TWB platform operates in the context of the sequence data analysis of TWB&#039;s R&amp;D projects. The service offer of the TWB bioinformatics platform includes the de novo assembly of micro-organisms, re-sequencing and analysis of genomic variants and the differential expression analysis of genomes from RNAseq. TWB is also involved in metagenomics in order to [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":3754,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_schema_org_content_json":"","footnotes":""},"categories":[1],"tags":[],"class_list":["post-3707","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-news"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/posts\/3707","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/comments?post=3707"}],"version-history":[{"count":1,"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/posts\/3707\/revisions"}],"predecessor-version":[{"id":3747,"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/posts\/3707\/revisions\/3747"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/media\/3754"}],"wp:attachment":[{"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/media?parent=3707"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/categories?post=3707"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.toulouse-white-biotechnology.com\/en\/wp-json\/wp\/v2\/tags?post=3707"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}