title: ParDRe: faster parallel duplicated reads removal tool for sequencing studies.
abstract: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe, a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files. It uses a novel bitwise approach to compare the suffixes of DNA strings and employs hybrid MPI/multithreading to reduce runtime on multicore systems. We show that ParDRe is up to 27.29 times faster than Fulcrum (a representative state-of-the-art tool) on a platform with two 8-core Sandy-Bridge processors.
  
  
  
  Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/pardre/
  
  
  
  jgonzalezd@udc.es.
authors.affiliation: Grupo de Arquitectura de Computadores, Universidade da Coruña, Campus De Elviña, 15071, A Coruña, Spain and.
authors.forename: Jorge
authors.initials: J
authors.lastname: González-Domínguez
authors.affiliation: Parallel and Distributed Architectures Group, Johannes Gutenberg University Mainz, 55128 Mainz, Germany.
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA / Q000379:methods*