Improving ancient DNA read mapping against modern reference genomes
Open accessAbstract
Background: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. Results: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. Conclusions: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.
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Using bwa aln with very relaxed parameters (-n 0.01 -o 2) in combination with disabling seeding (-l 1024) and mapQ 25 filtering had a beneficial impact in sensitivity (99.60% vs 97.34% for mapping reads containing the alternate allele) and a more balanced alternate allele representation (0.49936) but also increases error rates, for example increasing the rate of false mapping short microbial reads
“This had a beneficial impact in terms of sensitivity (99.60% vs 97.34% for the mapping of reads containing the alternate allele) and a more balanced alternate allele representation (0.49936) but also increases error rates, for example increasing the rate of false mapping short microbial reads (Additional file 1: Fig. S9).”
From Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (2020) · cites this paper as [13]
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Experimental — accuracy not yet measuredDecreasing the -n edit distance parameter in bwa aln from the default value of 0.04 to 0.02 or 0.01 allows more mismatches and increases sensitivity.
“decreasing the -n edit distance parameter from the default value of 0.04 to 0.02 [13] or 0.01 [14] allows more mismatches and increases sensitivity”
From Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (2020) · cites this paper as [13]
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A 5700 year-old human genome and oral microbiome from chewed birch pitch
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gargammel: a sequence simulator for ancient DNA
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Self-citationPalaeogenomic insights into the origins of French grapevine diversity
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“…et al., 1999) using the Burrows Wheeler Aligner (BWA aln) v. 0.7.5 (Li and Durbin, 2009) with default parameters except that seeding was disabled ( 2 1 1000) and edit distance was increased (-n 0.01) to improve mapping accuracy of ancient DNA reads, as recommended by (Schubert et al., 2012).”
InfluentialHigh‐Throughput DNA sequencing of ancient wood
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Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA
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Assessing DNA sequence alignment methods for characterizing ancient genomes and methylomes
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Shotgun microbial profiling of fossil remains
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Self-citationAncient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge
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Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland
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Self-citationThe efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains
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Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics
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Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes
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Ancient pathogen DNA in human teeth and petrous bones
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Self-citationComponents of a Neanderthal gut microbiome recovered from fecal sediments from El Salt
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- Authors
- Schubert, M., Ginolhac, A., Lindgreen, S., Thompson, J. F., AL-Rasheid, K. A., Willerslev, E., Krogh, A., & Orlando, L.
- Affiliations
- University of Copenhagen (DK)
- Helicos Biosciences (United States) (US)
- Corresponding author
- Orlando, Ludovic
- Venue
- BMC Genomics
- Published
- 2012-05-10
- Volume
- 13
- Issue
- 1
- Pages
- 178-178
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC3468387
- OpenAlex
- W2034552366
- Cited by
- 325
- References
- 34
- Citations by year
- 2026: 22 · 2025: 34 · 2024: 25 · 2023: 24 · 2022: 26 · 2021: 38 · 2020: 34 · 2019: 19 · 2018: 25 · 2017: 12 · 2016: 25 · 2015: 12 · 2014: 20 · 2013: 9
- FWCI
- 5.28
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Genomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Open Repository and Bibliography (University of Luxembourg) (submittedVersion)
- Funders
- National Research Foundation
- Danmarks Grundforskningsfond
- King Saud University
- Lundbeckfonden (R109-2012-9995, R70-2010-6286, R38-2008-3048, R24-2008-2527)
- Novo Nordisk
- Danmarks Frie Forskningsfond
- Novo Nordisk Fonden
- National Institutes of Health
- National Human Genome Research Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Arts and Humanities › Archeology › Paleopathology and ancient diseases
- Keywords
- ancient DNA, read mapping, reference genome alignment, sequencing errors, read trimming, Pleistocene horses, shotgun sequencing
- MeSH terms
- DNA Damage, Fossils, Genotype, Humans, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing
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