{"id":722,"date":"2015-01-13T20:00:58","date_gmt":"2015-01-13T20:00:58","guid":{"rendered":"https:\/\/blogs.bmj.com\/jmg\/?p=722"},"modified":"2026-02-25T01:15:06","modified_gmt":"2026-02-25T01:15:06","slug":"seqhbase-a-big-data-toolset-for-family-based-sequencing-data-analysis","status":"publish","type":"post","link":"https:\/\/blogs.bmj.com\/jmg\/2015\/01\/13\/seqhbase-a-big-data-toolset-for-family-based-sequencing-data-analysis\/","title":{"rendered":"SeqHBase: a big data toolset for family-based sequencing data analysis (Contributed by Min He, Ph.D.)"},"content":{"rendered":"<p>High-throughput sequencing technologies are now increasingly used to find disease genes, but it is difficult to infer biological insights from massive amounts of data in a short period of time. We developed a software framework called SeqHBase to help quickly identify disease genes. SeqHBase was developed based on Apache <a href=\"http:\/\/hadoop.apache.org\/\">Hadoop<\/a> and <a href=\"http:\/\/hbase.apache.org\/\">HBase<\/a> infrastructure, which works through distributed and parallel manner over multiple data nodes. Its input includes coverage information of 3 billion sites, over 3 million variants and their associated functional annotations for each genome. With 20 data nodes, SeqHBase took about 5 seconds for analyzing whole-exome sequencing data for a family quartet and approximately 1 minute for analyzing whole-genome sequencing data for a 10-member family. We demonstrated SeqHBase\u2019s high efficiency and scalability with several real sequencing data sets. (<a href=\"http:\/\/jmg.bmj.com\/content\/early\/2015\/01\/13\/jmedgenet-2014-102907\">http:\/\/jmg.bmj.com\/content\/early\/2015\/01\/13\/jmedgenet-2014-102907<\/a> )<!--TrendMD v2.4.8--><\/p>\n","protected":false},"excerpt":{"rendered":"<p>High-throughput sequencing technologies are now increasingly used to find disease genes, but it is difficult to infer biological insights from massive amounts of data in a short period of time. We developed a software framework called SeqHBase to help quickly identify disease genes. SeqHBase was developed based on Apache Hadoop and HBase infrastructure, which works [&#8230;]<\/p>\n<p><a class=\"btn btn-secondary understrap-read-more-link\" href=\"https:\/\/blogs.bmj.com\/jmg\/2015\/01\/13\/seqhbase-a-big-data-toolset-for-family-based-sequencing-data-analysis\/\">Read More&#8230;<\/a><\/p>\n","protected":false},"author":123,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-722","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>SeqHBase: a big data toolset for family-based sequencing data analysis (Contributed by Min He, Ph.D.) - JMG Contact blog<\/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:\/\/blogs.bmj.com\/jmg\/2015\/01\/13\/seqhbase-a-big-data-toolset-for-family-based-sequencing-data-analysis\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"SeqHBase: a big data toolset for family-based sequencing data analysis (Contributed by Min He, Ph.D.) - JMG Contact blog\" \/>\n<meta property=\"og:description\" content=\"High-throughput sequencing technologies are now increasingly used to find disease genes, but it is difficult to infer biological insights from massive amounts of data in a short period of time. We developed a software framework called SeqHBase to help quickly identify disease genes. 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