{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T18:21:09Z","timestamp":1772907669723,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1704,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps.<\/jats:p>\n               <jats:p>Availability: Available under the open-source MIT license at http:\/\/sourceforge.net\/projects\/hadoop-bam\/<\/jats:p>\n               <jats:p>Contact: \u00a0matti.niemenmaa@aalto.fi<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary material is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts054","type":"journal-article","created":{"date-parts":[[2012,2,3]],"date-time":"2012-02-03T01:42:17Z","timestamp":1328233337000},"page":"876-877","source":"Crossref","is-referenced-by-count":113,"title":["Hadoop-BAM: directly manipulating next generation sequencing data in the cloud"],"prefix":"10.1093","volume":"28","author":[{"given":"Matti","family":"Niemenmaa","sequence":"first","affiliation":[{"name":"1 Aalto University, Department of Information and Computer Science, PO Box 15400, FI-00076 Aalto, Finland and 2CSC\u2014IT Center for Science Ltd., PO Box 405, FI-02101 Espoo, Finland"}]},{"given":"Aleksi","family":"Kallio","sequence":"additional","affiliation":[{"name":"1 Aalto University, Department of Information and Computer Science, PO Box 15400, FI-00076 Aalto, Finland and 2CSC\u2014IT Center for Science Ltd., PO Box 405, FI-02101 Espoo, Finland"}]},{"given":"Andr\u00e9","family":"Schumacher","sequence":"additional","affiliation":[{"name":"1 Aalto University, Department of Information and Computer Science, PO Box 15400, FI-00076 Aalto, Finland and 2CSC\u2014IT Center for Science Ltd., PO Box 405, FI-02101 Espoo, Finland"}]},{"given":"Petri","family":"Klemel\u00e4","sequence":"additional","affiliation":[{"name":"1 Aalto University, Department of Information and Computer Science, PO Box 15400, FI-00076 Aalto, Finland and 2CSC\u2014IT Center for Science Ltd., PO Box 405, FI-02101 Espoo, Finland"}]},{"given":"Eija","family":"Korpelainen","sequence":"additional","affiliation":[{"name":"1 Aalto University, Department of Information and Computer Science, PO Box 15400, FI-00076 Aalto, Finland and 2CSC\u2014IT Center for Science Ltd., PO Box 405, FI-02101 Espoo, Finland"}]},{"given":"Keijo","family":"Heljanko","sequence":"additional","affiliation":[{"name":"1 Aalto University, Department of Information and Computer Science, PO Box 15400, FI-00076 Aalto, Finland and 2CSC\u2014IT Center for Science Ltd., PO Box 405, FI-02101 Espoo, Finland"}]}],"member":"286","published-online":{"date-parts":[[2012,2,2]]},"reference":[{"key":"2023012512203014400_B1","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1145\/1327452.1327492","article-title":"MapReduce: simplified data processing on large clusters","volume":"51","author":"Dean","year":"2008","journal-title":"Commun. of the ACM 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