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Evaluation of the impact of Illumina error correction tools on de novo genome assembly

Mahdi Heydari, Giles Miclotte (UGent) , Piet Demeester (UGent) , Yves Van de Peer (UGent) and Jan Fostier (UGent)
(2017) BMC BIOINFORMATICS. 18.
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Abstract
Background: Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced error rate in the input data. Surprisingly, a systematic validation of this assumption using state-of-the-art assembly methods is lacking, even for recently published methods. Results: For twelve recent Illumina error correction tools (EC tools) we evaluated both their ability to correct sequencing errors and their ability to improve de novo genome assembly in terms of contig size and accuracy. Conclusions: We confirm that most EC tools reduce the number of errors in sequencing data without introducing many new errors. However, we found that many EC tools suffer from poor performance in certain sequence contexts such as regions with low coverage or regions that contain short repeated or low-complexity sequences. Reads overlapping such regions are often ill-corrected in an inconsistent manner, leading to breakpoints in the resulting assemblies that are not present in assemblies obtained from uncorrected data. Resolving this systematic flaw in future EC tools could greatly improve the applicability of such tools.
Keywords
Next-generation sequencing, Error correction, Illumina, Genome assembly, ACCURATE CORRECTION, SEQUENCING ERRORS, MEMORY-EFFICIENT, BRUIJN GRAPHS, READS, ALIGNMENT

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MLA
Heydari, Mahdi, et al. “Evaluation of the Impact of Illumina Error Correction Tools on de Novo Genome Assembly.” BMC BIOINFORMATICS, vol. 18, 2017, doi:10.1186/s12859-017-1784-8.
APA
Heydari, M., Miclotte, G., Demeester, P., Van de Peer, Y., & Fostier, J. (2017). Evaluation of the impact of Illumina error correction tools on de novo genome assembly. BMC BIOINFORMATICS, 18. https://doi.org/10.1186/s12859-017-1784-8
Chicago author-date
Heydari, Mahdi, Giles Miclotte, Piet Demeester, Yves Van de Peer, and Jan Fostier. 2017. “Evaluation of the Impact of Illumina Error Correction Tools on de Novo Genome Assembly.” BMC BIOINFORMATICS 18. https://doi.org/10.1186/s12859-017-1784-8.
Chicago author-date (all authors)
Heydari, Mahdi, Giles Miclotte, Piet Demeester, Yves Van de Peer, and Jan Fostier. 2017. “Evaluation of the Impact of Illumina Error Correction Tools on de Novo Genome Assembly.” BMC BIOINFORMATICS 18. doi:10.1186/s12859-017-1784-8.
Vancouver
1.
Heydari M, Miclotte G, Demeester P, Van de Peer Y, Fostier J. Evaluation of the impact of Illumina error correction tools on de novo genome assembly. BMC BIOINFORMATICS. 2017;18.
IEEE
[1]
M. Heydari, G. Miclotte, P. Demeester, Y. Van de Peer, and J. Fostier, “Evaluation of the impact of Illumina error correction tools on de novo genome assembly,” BMC BIOINFORMATICS, vol. 18, 2017.
@article{8530189,
  abstract     = {{Background: Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced error rate in the input data. Surprisingly, a systematic validation of this assumption using state-of-the-art assembly methods is lacking, even for recently published methods. 
Results: For twelve recent Illumina error correction tools (EC tools) we evaluated both their ability to correct sequencing errors and their ability to improve de novo genome assembly in terms of contig size and accuracy. 
Conclusions: We confirm that most EC tools reduce the number of errors in sequencing data without introducing many new errors. However, we found that many EC tools suffer from poor performance in certain sequence contexts such as regions with low coverage or regions that contain short repeated or low-complexity sequences. Reads overlapping such regions are often ill-corrected in an inconsistent manner, leading to breakpoints in the resulting assemblies that are not present in assemblies obtained from uncorrected data. Resolving this systematic flaw in future EC tools could greatly improve the applicability of such tools.}},
  articleno    = {{374}},
  author       = {{Heydari, Mahdi and Miclotte, Giles and Demeester, Piet and Van de Peer, Yves and Fostier, Jan}},
  issn         = {{1471-2105}},
  journal      = {{BMC BIOINFORMATICS}},
  keywords     = {{Next-generation sequencing,Error correction,Illumina,Genome assembly,ACCURATE CORRECTION,SEQUENCING ERRORS,MEMORY-EFFICIENT,BRUIJN GRAPHS,READS,ALIGNMENT}},
  language     = {{eng}},
  pages        = {{13}},
  title        = {{Evaluation of the impact of Illumina error correction tools on de novo genome assembly}},
  url          = {{http://doi.org/10.1186/s12859-017-1784-8}},
  volume       = {{18}},
  year         = {{2017}},
}
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