{"id":5281,"date":"2024-07-28T23:38:16","date_gmt":"2024-07-28T21:38:16","guid":{"rendered":"https:\/\/nwww.crs4.it\/?p=5281"},"modified":"2025-04-29T16:55:52","modified_gmt":"2025-04-29T14:55:52","slug":"rapi","status":"publish","type":"post","link":"https:\/\/www.crs4.it\/en\/technology-catalogue\/rapi\/","title":{"rendered":"RAPI"},"content":{"rendered":"<p><script src=\"\/crs4_js\/people-details.js\"><\/script><\/p>\n<h3>Read Aligner API<\/h3>\n<div class=\"sm_hr\"><\/div>\n<h4>Contacts<\/h4>\n<div><a href=\"javascript:PeopleDetails.showAuthorDetails('148')\">Luca Pireddu<\/a>, Gianluigi Zanetti. E-mail:\u00a0<a class=\"linkurl\" href=\"mailto:valorisation@crs4.it\">valorisation@crs4.it<\/a><\/div>\n<h4>Challenge<\/h4>\n<p>Advancements in DNA read alignment algorithms have resulted in a number of read alignment tools that have different qualities and different APIs. Evaluating the various tools in the same pipeline can be challenging because of their incompatible interfaces. Moreover, these tools generally don\u2019t provide an easy-to-use programming interface to allow their seamless integration into novel software or workflows.<\/p>\n<h4>Overview<\/h4>\n<p>RAPI defines a C API for a short read aligner (to map short reads to a reference sequence) and high-level Python and Java interfaces. It also includes a reference implementation that wraps BWA-MEM and Python bindings for the API. RAPI can be used to integrate new read alignment software in existing RAPI-compliant software. It can also be used to allow simple Python scripting with standard read alignment algorithms or integration in JVM environments (Java, Scala, etc.).<\/p>\n<h4>Innovative features<\/h4>\n<ul>\n<li>standard multi-aligner API;<\/li>\n<li>high-level, high-performance Python interface.<\/li>\n<\/ul>\n<h4>Potential users<\/h4>\n<p>Bioinformaticians, researchers, sequencing centers professionals.<\/p>\n<h4>Impact sectors<\/h4>\n<p>Health &#8211; Biomedicine &#8211; ICT<\/p>\n<h4>Other resources<\/h4>\n<ol>\n<li><a href=\"https:\/\/github.com\/crs4\/rapi\">https:\/\/github.com\/crs4\/rapi<\/a><\/li>\n<li><a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btr325\" class=\"broken_link\">L.Pireddu, S. Leo, G. Zanetti; SEAL: a distributed short read mapping and duplicate removal tool, Bioinformatics, Volume 27, Issue 15, 1 August 2011, Pages 2159\u20132160, https:\/\/doi.org\/10.1093\/bioinformatics\/btr325<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Read Aligner API Contacts Luca Pireddu, Gianluigi Zanetti. E-mail:\u00a0valorisation@crs4.it Challenge Advancements in DNA read alignment algorithms have resulted in a number of read alignment tools that have different qualities and different APIs. Evaluating the various tools in the same pipeline can be challenging because of their incompatible interfaces. Moreover, these tools generally don\u2019t provide an [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[93,90],"tags":[],"class_list":["post-5281","post","type-post","status-publish","format-standard","hentry","category-life-sciences","category-technology-catalogue"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.9 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>RAPI - CRS4<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.crs4.it\/en\/technology-catalogue\/rapi\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"RAPI - CRS4\" \/>\n<meta property=\"og:description\" content=\"Read Aligner API Contacts Luca Pireddu, Gianluigi Zanetti. 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