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

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 f...

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Bibliographic Details
Published in:Genome biology 2025-01, Vol.26 (1), p.6-23, Article 6
Main Authors: Koptekin, Dilek, Yapar, Etka, Vural, Kıvılcım Başak, Sağlıcan, Ekin, Altınışık, N Ezgi, Malaspinas, Anna-Sapfo, Alkan, Can, Somel, Mehmet
Format: Article
Language:English
Subjects:
Algorithms
Ancient DNA
DNA, Ancient - analysis
Genome, Human
Genomics - methods
Graph-reference genome
Humans
Masking
Post-mortem damage
Reference bias
Software
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Summary: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.
ISSN:1474-760X
1474-760X
DOI:10.1186/s13059-024-03462-w