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

Date

2025-01-09

Author

Koptekin, Dilek
Yapar, Etka
Vural, Kıvılcım Başak
Sağlıcan, Ekin
ALTINIŞIK, NEFİZE EZGİ
Malaspinas, Anna-Sapfo
Alkan, Can
Somel, Mehmet

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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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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 raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.com/etkayapar/bamRefine and zenodo.org/records/14234666), masking reads only at positions possibly affected by PMD. We propose graph alignment coupled with bamRefine as a simple strategy to minimize data loss and bias, and urge the community to publish FASTQ files.

Subject Keywords

Ancient DNA, Graph-reference genome, Masking, Post-mortem damage, Reference bias

URI

https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85214866425&origin=inward
https://hdl.handle.net/11511/113145

Collections

Department of Biology, Article