Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data

Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data

Abstract We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from r...

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Bibliographic Details
Main Authors: Dilek Koptekin, Etka Yapar, Kıvılcım Başak Vural, Ekin Sağlıcan, N. Ezgi Altınışık, Anna-Sapfo Malaspinas, Can Alkan, Mehmet Somel
Format: Article
Language:English
Published: BMC 2025-01-01
Series:Genome Biology
Subjects:
Ancient DNA
Reference bias
Graph-reference genome
Post-mortem damage
Masking
Online Access:https://doi.org/10.1186/s13059-024-03462-w
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