{"id":5249,"date":"2024-07-28T23:36:11","date_gmt":"2024-07-28T21:36:11","guid":{"rendered":"https:\/\/nwww.crs4.it\/?p=5249"},"modified":"2025-04-29T00:56:15","modified_gmt":"2025-04-28T22:56:15","slug":"jeenk","status":"publish","type":"post","link":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/","title":{"rendered":"JEENK"},"content":{"rendered":"<p><script src=\"\/crs4_js\/people-details.js\"><\/script><\/p>\n<h3>JEENK<\/h3>\n<h3>Scalable genomics tools powered by Apache Flink<\/h3>\n<div class=\"sm_hr\"><\/div>\n<h4>Contacts<\/h4>\n<div><a href=\"javascript:PeopleDetails.showAuthorDetails('425')\">Francesco Versaci<\/a>,\u00a0<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>The rapid advancement of DNA and RNA sequencing technologies generates an exponential increase in the data stream to be processed by sequencing centers. New large-scale applications are enabled by the falling cost of data acquisition, but hindered by the use of conventional computational techniques used to process the data.<\/p>\n<h4>Overview<\/h4>\n<p>Jeenk is a collection of parallel, distributed tools for genomics, that introduce the distributed stream computing approach to large-scale genomics data analysis. Jeenk is based on the Apache Flink data streaming framework and uses Apache Kafka for data movement.<\/p>\n<p>It consists of three Flink-based tools that implement a full raw-to-CRAM pipeline for Illumina data:<\/p>\n<ul>\n<li>A reader, that reads the proprietary raw Illumina BCL files directly from the sequencer&#8217;s run directory and converts them to read-based data (FASTQ-like), which are sent to a Kafka broker for storage and further processing (akin to Illumina&#8217;s bcl2fastq2);<\/li>\n<li>An aligner, that aligns the reads to a reference genome using the BWA-MEM plugin through the RAPI library (http:\/\/github.com\/crs4\/rapi\/);<\/li>\n<li>A CRAM writer, that writes the aligned reads as space-efficient CRAM files.<\/li>\n<\/ul>\n<h4>Innovative features<\/h4>\n<ul>\n<li>ultra-scalable state-of-the-art distributed stream processing technology;<\/li>\n<li>reduced turnaround times.<\/li>\n<\/ul>\n<h4>Potential users<\/h4>\n<p>Bioinformatics researchers, sequencing centers professionals<\/p>\n<h4>Impact sectors<\/h4>\n<p>Biotechnologies<\/p>\n<h4>Other resources<\/h4>\n<ol>\n<li><a href=\"https:\/\/github.com\/crs4\/Jeenk\">https:\/\/github.com\/crs4\/Jeenk<\/a><\/li>\n<li><a href=\"http:\/\/dx.doi.org\/10.1109\/BigData.2016.7840727\" class=\"broken_link\">F. Versaci, L. Pireddu, G. Zanetti, &#8220;Scalable genomics: From raw data to aligned reads on Apache YARN&#8221;, Proc. IEEE Int. Conf. Big Data (Big Data), pp. 1232-1241, Dec. 2016.<\/a><\/li>\n<li><a href=\"http:\/\/publications.crs4.it\/pubdocs\/2018\/VPZ18\/private\/VersaciPZ18.pdf\">F. Versaci, L. Pireddu, G. Zanetti, Proc. IEEE EMBS Int. Conf. on Biomedical &amp; Health Informatics (BHI), Vol. 2018, pp. 259-262, 2018<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>JEENK Scalable genomics tools powered by Apache Flink Contacts Francesco Versaci,\u00a0Luca Pireddu, Gianluigi Zanetti. E-mail:\u00a0valorisation@crs4.it Challenge The rapid advancement of DNA and RNA sequencing technologies generates an exponential increase in the data stream to be processed by sequencing centers. New large-scale applications are enabled by the falling cost of data acquisition, but hindered by the [&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-5249","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>JEENK - 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\/jeenk\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"JEENK - CRS4\" \/>\n<meta property=\"og:description\" content=\"JEENK Scalable genomics tools powered by Apache Flink Contacts Francesco Versaci,\u00a0Luca Pireddu, Gianluigi Zanetti. E-mail:\u00a0valorisation@crs4.it Challenge The rapid advancement of DNA and RNA sequencing technologies generates an exponential increase in the data stream to be processed by sequencing centers. New large-scale applications are enabled by the falling cost of data acquisition, but hindered by the [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/\" \/>\n<meta property=\"og:site_name\" content=\"CRS4\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/pages\/CRS4\/153623948010688\" \/>\n<meta property=\"article:published_time\" content=\"2024-07-28T21:36:11+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-04-28T22:56:15+00:00\" \/>\n<meta name=\"author\" content=\"Paolo Sirigu\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/\"},\"author\":{\"name\":\"Paolo Sirigu\",\"@id\":\"https:\/\/www.crs4.it\/en\/#\/schema\/person\/d6d18aa42b5f98236124cab354b7f22f\"},\"headline\":\"JEENK\",\"datePublished\":\"2024-07-28T21:36:11+00:00\",\"dateModified\":\"2025-04-28T22:56:15+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/\"},\"wordCount\":278,\"publisher\":{\"@id\":\"https:\/\/www.crs4.it\/en\/#organization\"},\"articleSection\":[\"life sciences\",\"Technology catalogue\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/\",\"url\":\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/\",\"name\":\"JEENK - CRS4\",\"isPartOf\":{\"@id\":\"https:\/\/www.crs4.it\/en\/#website\"},\"datePublished\":\"2024-07-28T21:36:11+00:00\",\"dateModified\":\"2025-04-28T22:56:15+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/www.crs4.it\/en\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"JEENK\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/www.crs4.it\/en\/#website\",\"url\":\"https:\/\/www.crs4.it\/en\/\",\"name\":\"CRS4\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/www.crs4.it\/en\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/www.crs4.it\/en\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/www.crs4.it\/en\/#organization\",\"name\":\"CRS4\",\"url\":\"https:\/\/www.crs4.it\/en\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.crs4.it\/en\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/www.crs4.it\/wp-content\/uploads\/CRS4.trentennale_3.png\",\"contentUrl\":\"https:\/\/www.crs4.it\/wp-content\/uploads\/CRS4.trentennale_3.png\",\"width\":1518,\"height\":577,\"caption\":\"CRS4\"},\"image\":{\"@id\":\"https:\/\/www.crs4.it\/en\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/www.facebook.com\/pages\/CRS4\/153623948010688\",\"https:\/\/www.instagram.com\/crs4.it\/\",\"https:\/\/www.youtube.com\/CRS4video\",\"https:\/\/www.linkedin.com\/company\/crs4\",\"https:\/\/www.slideshare.net\/CRS4\"]},{\"@type\":\"Person\",\"@id\":\"https:\/\/www.crs4.it\/en\/#\/schema\/person\/d6d18aa42b5f98236124cab354b7f22f\",\"name\":\"Paolo Sirigu\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.crs4.it\/en\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/b8b44484d86fad28cb7ed89c8cf7ca1057f60adcf3113c1a0f24d057dbf8005d?s=96&d=mm&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/b8b44484d86fad28cb7ed89c8cf7ca1057f60adcf3113c1a0f24d057dbf8005d?s=96&d=mm&r=g\",\"caption\":\"Paolo Sirigu\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"JEENK - CRS4","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/","og_locale":"en_US","og_type":"article","og_title":"JEENK - CRS4","og_description":"JEENK Scalable genomics tools powered by Apache Flink Contacts Francesco Versaci,\u00a0Luca Pireddu, Gianluigi Zanetti. E-mail:\u00a0valorisation@crs4.it Challenge The rapid advancement of DNA and RNA sequencing technologies generates an exponential increase in the data stream to be processed by sequencing centers. New large-scale applications are enabled by the falling cost of data acquisition, but hindered by the [&hellip;]","og_url":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/","og_site_name":"CRS4","article_publisher":"https:\/\/www.facebook.com\/pages\/CRS4\/153623948010688","article_published_time":"2024-07-28T21:36:11+00:00","article_modified_time":"2025-04-28T22:56:15+00:00","author":"Paolo Sirigu","twitter_card":"summary_large_image","schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/#article","isPartOf":{"@id":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/"},"author":{"name":"Paolo Sirigu","@id":"https:\/\/www.crs4.it\/en\/#\/schema\/person\/d6d18aa42b5f98236124cab354b7f22f"},"headline":"JEENK","datePublished":"2024-07-28T21:36:11+00:00","dateModified":"2025-04-28T22:56:15+00:00","mainEntityOfPage":{"@id":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/"},"wordCount":278,"publisher":{"@id":"https:\/\/www.crs4.it\/en\/#organization"},"articleSection":["life sciences","Technology catalogue"],"inLanguage":"en-US"},{"@type":"WebPage","@id":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/","url":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/","name":"JEENK - CRS4","isPartOf":{"@id":"https:\/\/www.crs4.it\/en\/#website"},"datePublished":"2024-07-28T21:36:11+00:00","dateModified":"2025-04-28T22:56:15+00:00","breadcrumb":{"@id":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.crs4.it\/en\/technology-catalogue\/jeenk\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.crs4.it\/en\/"},{"@type":"ListItem","position":2,"name":"JEENK"}]},{"@type":"WebSite","@id":"https:\/\/www.crs4.it\/en\/#website","url":"https:\/\/www.crs4.it\/en\/","name":"CRS4","description":"","publisher":{"@id":"https:\/\/www.crs4.it\/en\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.crs4.it\/en\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/www.crs4.it\/en\/#organization","name":"CRS4","url":"https:\/\/www.crs4.it\/en\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.crs4.it\/en\/#\/schema\/logo\/image\/","url":"https:\/\/www.crs4.it\/wp-content\/uploads\/CRS4.trentennale_3.png","contentUrl":"https:\/\/www.crs4.it\/wp-content\/uploads\/CRS4.trentennale_3.png","width":1518,"height":577,"caption":"CRS4"},"image":{"@id":"https:\/\/www.crs4.it\/en\/#\/schema\/logo\/image\/"},"sameAs":["https:\/\/www.facebook.com\/pages\/CRS4\/153623948010688","https:\/\/www.instagram.com\/crs4.it\/","https:\/\/www.youtube.com\/CRS4video","https:\/\/www.linkedin.com\/company\/crs4","https:\/\/www.slideshare.net\/CRS4"]},{"@type":"Person","@id":"https:\/\/www.crs4.it\/en\/#\/schema\/person\/d6d18aa42b5f98236124cab354b7f22f","name":"Paolo Sirigu","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.crs4.it\/en\/#\/schema\/person\/image\/","url":"https:\/\/secure.gravatar.com\/avatar\/b8b44484d86fad28cb7ed89c8cf7ca1057f60adcf3113c1a0f24d057dbf8005d?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/b8b44484d86fad28cb7ed89c8cf7ca1057f60adcf3113c1a0f24d057dbf8005d?s=96&d=mm&r=g","caption":"Paolo Sirigu"}}]}},"_links":{"self":[{"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/posts\/5249","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/comments?post=5249"}],"version-history":[{"count":1,"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/posts\/5249\/revisions"}],"predecessor-version":[{"id":5250,"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/posts\/5249\/revisions\/5250"}],"wp:attachment":[{"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/media?parent=5249"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/categories?post=5249"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.crs4.it\/en\/wp-json\/wp\/v2\/tags?post=5249"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}