ParDRe: faster parallel duplicated reads removal tool for sequencing studies

Bioinformatics
Jorge González-Domínguez, Bertil Schmidt

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.

References

Jun 24, 2011·Bioinformatics·Luca PiredduGianluigi Zanetti
Mar 16, 2012·Bioinformatics·Matthew S BurriesciJohn R Pringle
Jan 30, 2014·Molecular Ecology·Xiaofan Zhou, Antonis Rokas
Mar 26, 2015·Frontiers in Bioengineering and Biotechnology·Andrea ManconiLuciano Milanesi

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Citations

May 6, 2017·Bioinformatics·Roberto R ExpósitoJuan Touriño
Jan 31, 2020·Bioinformatics·Gianvito UrgeseElisa Ficarra
Aug 14, 2019·Scientific Reports·Antonio Sérgio Cruz GaiaAdonney Allan de Oliveira Veras
Oct 4, 2017·Nucleic Acids Research·Shaoliang PengFei Li
Oct 5, 2019·Communications Biology·Maeva A TecherAlexander S Mikheyev
Jan 12, 2020·Communications Biology·Maeva A TecherAlexander S Mikheyev

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