{"id":193,"date":"2024-12-17T16:04:04","date_gmt":"2024-12-17T15:04:04","guid":{"rendered":"https:\/\/project.inria.fr\/omicfinder\/?page_id=193"},"modified":"2025-11-24T08:06:51","modified_gmt":"2025-11-24T07:06:51","slug":"realizations","status":"publish","type":"page","link":"https:\/\/project.inria.fr\/omicfinder\/realizations\/","title":{"rendered":"Realizations"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\"><a href=\"http:\/\/logan-search.org\">Logan Search<\/a><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">In collaboration with <a href=\"https:\/\/tlemane.github.io\/\">T\u00e9o Lemane<\/a> from CEA <a href=\"https:\/\/jacob.cea.fr\/drf\/ifrancoisjacob\/Pages\/Departements\/Genoscope.aspx\" target=\"_blank\" rel=\"noreferrer noopener\">Genoscope<\/a>, with our partner <a href=\"https:\/\/research.pasteur.fr\/en\/member\/rayan-chikhi\/\" target=\"_blank\" rel=\"noreferrer noopener\">Rayan Chikhi<\/a> from the <a href=\"https:\/\/research.pasteur.fr\/en\/team\/sequence-bioinformatics\/\" target=\"_blank\" rel=\"noreferrer noopener\">Sequences Bioinformatics<\/a>\u00a0team at Pasteur Institute, and the <a href=\"https:\/\/rrna.ca\/\">Artem Babaian<\/a>&#8216;s group we introduced &#8220;<a href=\"http:\/\/logan-search.org\">Logan Search<\/a>&#8221; [1] which allows you to search for any DNA sequence in minutes, bringing Earth\u2019s largest genomic resource to your fingertips.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Under the hood, we built a 1 petabyte k-mer index for all 27 million sequencing datasets in the SRA up to 12-2023.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Logan Search transforms your query to its k-mers (k=31), and in the time it takes to brew a coffee, it will retrieve every dataset containing your k-mers. It\u2019s the only service working at this scale.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The output datasets are easily visualized with custom plots in Logan Search, which accesses a harmonized set of query and SRA meta-data including sequencing technology, type of molecule, geographic distribution, and sample origins. Learn more about your sequence.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Logan Search returns a list of SRA accessions, not alignments. To bring you closer to the data we\u2019ve also created a microservice to instantly retrieve Logan contigs matching your search.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">[1] Chikhi, R., Lemane, T., Loll-Krippleber, R., Montoliu-Nerin, M., Raffestin, B., Camargo, A. P., &#8230; &amp; Babaian, A. (2024). Logan: planetary-scale genome assembly surveys life\u2019s diversity.\u00a0<em>bioRxiv<\/em>, 2024-07.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><a href=\"https:\/\/github.com\/yhhshb\/kaminari\">Kaminari<\/a><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">With <em>Kaminari<\/em> [2] explore a new index design based on minimizers and integer compression methods. We show that a careful implementation of this design outperforms previous solutions based on Bloom filters by a wide margin.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">[2] Levallois, V., Shibuya, Y., Le Gal, B., Patro, R., Peterlongo, P., &amp; Pibiri, G. E. (2025). Kaminari: a resource-frugal index for approximate colored k-mer queries.\u00a0<em>bioRxiv<\/em>, 2025-05.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><a href=\"https:\/\/github.com\/pierrepeterlongo\/back_to_sequences\">Back to sequences<\/a> <\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">We proposed a simple yet useful tool when dealing with large genomic datasets. This is &#8220;<em>Back to sequences: Find the origin of k-mers<\/em> [3]&#8221;.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">[3] Baire et al., (2024). Back to sequences: Find the origin of k-mers. Journal of Open Source Software, 9(101), 7066, <a href=\"https:\/\/doi.org\/10.21105\/joss.07066\">https:\/\/doi.org\/10.21105\/joss.07066<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Logan Search In collaboration with T\u00e9o Lemane from CEA Genoscope, with our partner Rayan Chikhi from the Sequences Bioinformatics\u00a0team at Pasteur Institute, and the Artem Babaian&#8216;s group we introduced &#8220;Logan Search&#8221; [1] which allows you to search for any DNA sequence in minutes, bringing Earth\u2019s largest genomic resource to your\u2026<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/project.inria.fr\/omicfinder\/realizations\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":311,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_members_access_role":[],"_members_access_error":""},"class_list":["post-193","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/pages\/193","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/users\/311"}],"replies":[{"embeddable":true,"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/comments?post=193"}],"version-history":[{"count":6,"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/pages\/193\/revisions"}],"predecessor-version":[{"id":243,"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/pages\/193\/revisions\/243"}],"wp:attachment":[{"href":"https:\/\/project.inria.fr\/omicfinder\/wp-json\/wp\/v2\/media?parent=193"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}