Introduction

MOTIVATION: 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. CONCLUSION: 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. Fiona: a parallel and automatic strategy for read error correction.
    Cite this
    Schulz MH, Weese D, Holtgrewe M, Dimitrova V, Niu S, Reinert K, Richard H, 2014-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Marcel H Schulz
    Developer

    'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, France

  2. David Weese
    Developer

    'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, France

  3. Manuel Holtgrewe
    Developer

    'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, France

  4. Viktoria Dimitrova
    Developer

    'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, France

  5. Sijia Niu
    Developer

    'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, France

  6. Knut Reinert
    Developer

    'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, France

  7. Hugues Richard
    Investigator

    'Multimodal Computing and Interaction', Saarland University & Department for Computational Biology and Applied Computing, France

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Summary
AccessionBT006585
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionFrance
Submitted ByHugues Richard