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001-es BibID:	BIBFORM117696
035-os BibID:	(cikkazonosító)1260486 (Scopus)85180226381 (WOS)001129408900001
Első szerző:	Lien, Annette
Cím:	Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA / Lien Annette, Legori Leonardo Pestana, Kraft Louis, Sackett Peter Wad, Renaud Gabriel
Dátum:	2023
ISSN:	2673-7647
Megjegyzések:	Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient DNA molecules, therefore the reads often contain some portion of the sequencing adaptors. It is crucial to remove those adaptors, as they can interfere with downstream analysis. Furthermore, overlapping portions when DNA has been read forward and backward (paired-end) can be merged to correct sequencing errors and improve read quality. Several tools have been developed for adapter trimming and read merging, however, no one has attempted to evaluate their accuracy and evaluate their potential impact on downstream analyses. Through the simulation of sequencing data, seven commonly used tools were analyzed in their ability to reconstruct ancient DNA sequences through read merging. The analyzed tools exhibit notable differences in their abilities to correct sequence errors and identify the correct read overlap, but the most substantial difference is observed in their ability to calculate quality scores for merged bases. Selecting the most appropriate tool for a given project depends on several factors, although some tools such as fastp have some shortcomings, whereas others like leeHom outperform the other tools in most aspects. While the choice of tool did not result in a measurable difference when analyzing population genetics using principal component analysis, it is important to note that downstream analyses that are sensitive to wrongly merged reads or that rely on quality scores can be significantly impacted by the choice of tool.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk adapter trimming ancient DNA benchmarking next-generation sequencing read merging read processing
Megjelenés:	Frontiers in Bioinformatics. - 3 (2023), p. 1-18. -
További szerzők:	Legori, Leonardo Pestana Kraft, Louis Sackett, Peter Wad Renaud, Gabriel
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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