Introduction

MOTIVATION: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections. RESULT: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k-mer spectrum. With high-quality k-mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. AVAILABILITY AND IMPLEMENTATION: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net. CONTACT: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. Trowel: a fast and accurate error correction module for Illumina sequencing reads.
    Cite this
    Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D, 2014-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Eun-Cheon Lim
    Developer

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Germany

  2. Jonas Müller
    Developer

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Germany

  3. Jörg Hagmann
    Developer

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Germany

  4. Stefan R Henz
    Developer

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Germany

  5. Sang-Tae Kim
    Developer

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Germany

  6. Detlef Weigel
    Investigator

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Germany

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Summary
AccessionBT001296
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByDetlef Weigel