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Evaluation of theimpact of Illuminaerror correctiontools on de novogenome assembly Mahdi HeydariGiles MiclottePiet Demeester2017 год

Evaluation of the impact of Illumina error correction tools on de novo genome assembly
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Аннотация: 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. 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. 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.
Год издания: 2017
Авторы: Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
Издательство: BioMed Central
Источник: BMC Bioinformatics
Ключевые слова: Genomics and Phylogenetic Studies, RNA and protein synthesis mechanisms, Chromosomal and Genetic Variations
Другие ссылки: BMC Bioinformatics (PDF)
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