Repository: Freie Universität Berlin, Math Department

Fiona: a parallel and automatic strategy for read error correction

Schulz, M. H. and Weese, D. and Holtgrewe, M. and Dimitrova, V. and Niu, S. and Reinert, K. and Richard, H. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics, 30 (17). i356-i363.

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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 or hugues.richard@upmc.frSupplementary information: Supplementary data are available at Bioinformatics online.

Item Type:Article
Subjects:Biological Sciences
Mathematical and Computer Sciences
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:1451
Deposited By: AG Alg BioInf
Deposited On:26 Aug 2014 14:02
Last Modified:03 Mar 2017 14:41

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