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

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 https://mardre.des.udc.es .

Contact: [email protected].