title: Trowel: a fast and accurate error correction module for Illumina sequencing reads.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  euncheon.lim@tue.mpg.de or weigel@tue.mpg.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors: Eun-Cheon
authors: EC
authors: Lim
authors: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors: Jonas
authors: J
authors: Müller
authors: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors: Jörg
authors: J
authors: Hagmann
authors: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors: Stefan R
authors: SR
authors: Henz
authors: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors: Sang-Tae
authors: ST
authors: Kim
authors: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors: Detlef
authors: D
authors: Weigel
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012984:Software