Fiona: A parallel and automatic strategy for read error correction

Bioinformatics

Volumn 30, Issue 17, 2014, Pages

  Schulz, Marcel H ^a,b   Weese, David ^c   Holtgrewe, Manuel ^c   Dimitrova, Viktoria ^d   Niu, Sijia ^d   Reinert, Knut ^c   Richard, Hugues ^d  

^a SAARLAND UNIVERSITY   (Germany)

^b CARNEGIE MELLON UNIVERSITY   (United States)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

^d UMR 7238   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; PROCEDURES;

ALGORITHMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INDEL MUTATION; SEQUENCE ANALYSIS, DNA;

FIONA;

EID: 84907027898     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu440     Document Type: Conference Paper

References (17)

1. Abouelhoda, M. et al. (2004) Replacing suffix trees with enhanced suffix arrays. J. Discrete Alg., 2, 53-86.
2. Chaisson, M.J. and Pevzner, P.A. (2008) Short read fragment assembly of bacterial genomes. Genome Res, 18, 324-330.
3. Döring, A. et al. (2008) SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9, 11.
4. Gnerre, S. et al. (2010) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PNAS, 108, 1513-1518.
5. Ilie, L. et al. (2011) HiTEC: Accurate error correction in high-throughput sequencing data. Bioinformatics, 27, 295-302.
6. Kao, W. et al. (2011) ECHO: A reference-free short-read error correction algorithm. Genome Res., 21, 1181-1192.
7. Kelley, D.R. et al. (2010) Quake: quality-Aware detection and correction of sequencing errors. Genome Biol., 11, R116.
8. Minoche, A. et al. (2011) Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems. Genome Biol., 12, R112.
9. Pevzner, P.A. et al. (2001) An eulerian path approach to dna fragment assembly. PNAS, 98, 9748-9753.
10. Quail, M. et al. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 341.
11. Salmela, L. (2010) Correction of sequencing errors in a mixed set of reads. Bioinformatics, 26, 1284-1290.
12. Salmela, L. and Schröder, J. (2011) Correcting errors in short reads by multiple alignments. Bioinformatics, 27, 1455-1461.
13. Salzberg, S.L. et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res., 22, 557-567.
14. Schröder, J. et al. (2009) SHREC: A short-read error correction method. Bioinformatics, 25, 2157-2163.
15. Wang, X.V. et al. (2012) Estimation of sequencing error rates in short reads. BMC Bioinformatics, 13, 185.
16. Yang, X. et al. (2010) Reptile: representative tiling for short read error correction. Bioinformatics, 26, 2526-2533.
17. Yang, X. et al. (2013) A survey of error-correction methods for next-generation sequencing. Brief. Bioinform., 14, 56-66.