ArticleGenome biology2025
Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome.Nature ecology & evolution · 2026Article
- Optimal Reference Panel Design in Ancient DNA Imputation from Coalescent Theory, Simulation, and Real Data Application with an Ancient Reference Panel.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the performance of ancient DNA genetic relatedness estimation methods using high-fidelity pedigree simulations.Genome biology · 2026Article
- A SNP panel for co-analysis of capture and shotgun ancient DNA data.bioRxiv : the preprint server for biology · 2025Article
- Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.G3 (Bethesda, Md.) · 2025Article
- Temporal Genomics Reveal a Century of Genomic Diversity Shifts Across a Biodiversity Hotspot Avian Assemblage.Genome biology and evolution · 2025Article
- Molecular Paleontology Meets Drug Discovery: The Case for De-extinct Antimicrobials.ACS omega · 2025Review
- The genomic footprints of migration: how ancient DNA reveals our history of mobility.Genome biology · 2025Review
- Improving data archiving practices in ancient genomics.Scientific data · 2024Article
- Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.