MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud

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Abstract

Summary:

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.

Availability and implementation:

Source code in Java and Hadoop as well as a user's guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es.

Contact:

rreye@udc.es

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