ArticleEcology and evolution2021
An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data.
Article in Ecology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
- Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (bioRxiv : the preprint server for biology · 2026Article
- The Genomic Legacy of the Norman Conquest in Rural England.bioRxiv : the preprint server for biology · 2026Article
- MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes.American journal of human genetics · 2026Article
- Genomic insights into ancestry and infectious disease in 17th-century colonial Brazil.bioRxiv : the preprint server for biology · 2025Article
- SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.NAR genomics and bioinformatics · 2025Article
- Anthropocene genetic diversity loss in the marine tropics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- MetaGLIMPSE: Meta Imputation of Low Coverage Sequencing Data for Modern and Ancient Genomes.bioRxiv : the preprint server for biology · 2025Article
- Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies.Molecular ecology resources · 2025Review
- Unravelling reference bias in ancient DNA datasets.Bioinformatics (Oxford, England) · 2024Article
- The genomic prehistory of the Indigenous peoples of Uruguay.PNAS nexus · 2022Article
- Additional evaluations show that specificEcology and evolution · 2021Article
- An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data.Ecology and evolution · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.
Indexed as
Identifiers
What OpenQuestion holds
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.