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http://hdl.handle.net/2183/20848 MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
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Roberto R. Expósito, Jorge Veiga, Jorge González-Domínguez, Juan Touriño; MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud, Bioinformatics, Volume 33, Issue 17, 1 September 2017, Pages 2762–2764, https://doi.org/10.1093/bioinformatics/btx307
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[Abstract] This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool.
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This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Roberto R. Expósito, Jorge Veiga, Jorge González-Domínguez, Juan Touriño; MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud, Bioinformatics, Volume 33, Issue 17, 1 September 2017, Pages 2762–2764 is available online at: https://doi.org/10.1093/bioinformatics/btx307