title: Fiona: a parallel and automatic strategy for read error correction.
abstract: BACKGROUND
  Automatic error correction of high-throughput sequencing data can have a dramatic impact on the amount of usable base pairs and their quality. It has been shown that the performance of tasks such as de novo genome assembly and SNP calling can be dramatically improved after read error correction. While a large number of methods specialized for correcting substitution errors as found in Illumina data exist, few methods for the correction of indel errors, common to technologies like 454 or Ion Torrent, have been proposed.
  
  
  RESULTS
  We present Fiona, a new stand-alone read error-correction method. Fiona provides a new statistical approach for sequencing error detection and optimal error correction and estimates its parameters automatically. Fiona is able to correct substitution, insertion and deletion errors and can be applied to any sequencing technology. It uses an efficient implementation of the partial suffix array to detect read overlaps with different seed lengths in parallel. We tested Fiona on several real datasets from a variety of organisms with different read lengths and compared its performance with state-of-the-art methods. Fiona shows a constantly higher correction accuracy over a broad range of datasets from 454 and Ion Torrent sequencers, without compromise in speed.
  
  
  CONCLUSIONS
  Fiona is an accurate parameter-free read error-correction method that can be run on inexpensive hardware and can make use of multicore parallelization whenever available. Fiona was implemented using the SeqAn library for sequence analysis and is publicly available for download at http://www.seqan.de/projects/fiona.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Schulz
authors.affiliation: 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.
authors.forename: David
authors.initials: D
authors.lastname: Weese
authors.affiliation: 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.
authors.forename: Manuel
authors.initials: M
authors.lastname: Holtgrewe
authors.affiliation: 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.
authors.forename: Viktoria
authors.initials: V
authors.lastname: Dimitrova
authors.affiliation: 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.
authors.forename: Sijia
authors.initials: S
authors.lastname: Niu
authors.affiliation: 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
authors.affiliation: 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France 'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, Max Planck Institute for Informatics, Saarbrücken, 66123 Saarland, Germany, Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15206 PA, USA, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany, Université Pierre et Marie Curie, UMR7238, CNRS-UPMC, Paris, France and CNRS, UMR7238, Laboratory of Computational and Quantitative Biology, Paris, France.
authors.forename: Hugues
authors.initials: H
authors.lastname: Richard
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054643:INDEL Mutation; D017422:Sequence Analysis, DNA / Q000379:methods*