Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data
Koptekin, Dilek ; Yapar, Etka LU
; Vural, Kıvılcım Başak
; Sağlıcan, Ekin
; Altınışık, N. Ezgi
; Malaspinas, Anna-Sapfo
; Alkan, Can
and Somel, Mehmet
(2025)
In Genome Biology
26.
- 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.
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/5db9574d-bf42-4cc8-84ed-86f3e517027d
- author
- Koptekin, Dilek
; Yapar, Etka
LU
; Vural, Kıvılcım Başak
; Sağlıcan, Ekin
; Altınışık, N. Ezgi
; Malaspinas, Anna-Sapfo
; Alkan, Can
and Somel, Mehmet
- organization
- publishing date
- 2025-01-09
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Ancient DNA (aDNA), reference bias, post-mortem damage
- in
- Genome Biology
- volume
- 26
- article number
- 6
- pages
- 23 pages
- publisher
- BioMed Central (BMC)
- external identifiers
-
- pmid:39789608
- scopus:85214866425
- ISSN
- 1474-760X
- DOI
- 10.1186/s13059-024-03462-w
- language
- English
- LU publication?
- yes
- id
- 5db9574d-bf42-4cc8-84ed-86f3e517027d
- date added to LUP
- 2025-01-27 11:44:21
- date last changed
- 2025-04-04 15:03:49
@article{5db9574d-bf42-4cc8-84ed-86f3e517027d,
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.}},
author = {{Koptekin, Dilek and Yapar, Etka and Vural, Kıvılcım Başak and Sağlıcan, Ekin and Altınışık, N. Ezgi and Malaspinas, Anna-Sapfo and Alkan, Can and Somel, Mehmet}},
issn = {{1474-760X}},
keywords = {{Ancient DNA (aDNA); reference bias; post-mortem damage}},
language = {{eng}},
month = {{01}},
publisher = {{BioMed Central (BMC)}},
series = {{Genome Biology}},
title = {{Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data}},
url = {{http://dx.doi.org/10.1186/s13059-024-03462-w}},
doi = {{10.1186/s13059-024-03462-w}},
volume = {{26}},
year = {{2025}},
}