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Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

https://doi.org/10.1101/782755
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Reconstructing the Deep Population History of Central and South America
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Genes mirror migrations and cultures in prehistoric Europe — a population genomic perspective
inferredcites →https://doi.org/10.1016/j.tig.2019.02.006openalex-snapshot
The Promise of Paleogenomics Beyond Our Own Species
inferredcites →https://doi.org/10.1016/j.tig.2019.11.006openalex-snapshot
Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications
inferredcites →https://doi.org/10.1038/nature08835openalex-snapshot
Ancient human genome sequence of an extinct Palaeo-Eskimo
inferredcites →https://doi.org/10.1038/nature13025openalex-snapshot
The genome of a Late Pleistocene human from a Clovis burial site in western Montana
inferredcites →https://doi.org/10.1038/nature13673openalex-snapshot
Ancient human genomes suggest three ancestral populations for present-day Europeans
inferredcites →https://doi.org/10.1038/nature13810openalex-snapshot
Genome sequence of a 45,000-year-old modern human from western Siberia
inferredcites →https://doi.org/10.1038/nature14507openalex-snapshot
Population genomics of Bronze Age Eurasia
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature19310openalex-snapshot
Genomic insights into the origin of farming in the ancient Near East
inferredcites →https://doi.org/10.1038/nbt.4227openalex-snapshot
Variation graph toolkit improves read mapping by representing genetic variation in the reference
inferredcites →https://doi.org/10.1038/ncomms10326openalex-snapshot
Genomic signals of migration and continuity in Britain before the Anglo-Saxons
inferredcites →https://doi.org/10.1038/ncomms10408openalex-snapshot
Iron Age and Anglo-Saxon genomes from East England reveal British migration history
inferredcites →https://doi.org/10.1038/ng1847openalex-snapshot
Principal components analysis corrects for stratification in genome-wide association studies
inferredcites →https://doi.org/10.1038/nrg3029openalex-snapshot
Learning about human population history from ancient and modern genomes
inferredcites →https://doi.org/10.1038/sj.gene.6364172openalex-snapshot
Detection of the CCR5-Δ32 HIV resistance gene in Bronze Age skeletons
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts503openalex-snapshot
Qualimap: evaluating next-generation sequencing alignment data
inferredcites →https://doi.org/10.1093/bioinformatics/btt193openalex-snapshot
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot
circlize implements and enhances circular visualization in R
inferredcites →https://doi.org/10.1093/bioinformatics/btv098openalex-snapshot
Sambamba: fast processing of NGS alignment formats
inferredcites →https://doi.org/10.1093/bioinformatics/btv112openalex-snapshot
Unified representation of genetic variants
inferredcites →https://doi.org/10.1093/bioinformatics/btw670openalex-snapshot
gargammel: a sequence simulator for ancient DNA
inferredcites →https://doi.org/10.1093/bioinformatics/bty507openalex-snapshot
snpAD: an ancient DNA genotype caller
inferredcites →https://doi.org/10.1093/bioinformatics/btz597openalex-snapshot
Sequence tube maps: making graph genomes intuitive to commuters
inferredcites →https://doi.org/10.1093/nar/gkp1163openalex-snapshot
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
inferredcites →https://doi.org/10.1098/rstb.2013.0624openalex-snapshot
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA
inferredcites →https://doi.org/10.1101/105346openalex-snapshot
ATLAS: Analysis Tools for Low-depth and Ancient Samples
inferredcites →https://doi.org/10.1101/cshperspect.a012567openalex-snapshot
Ancient DNA Damage
inferredcites →https://doi.org/10.1101/gr.214155.116openalex-snapshot
Genome graphs and the evolution of genome inference
inferredcites →https://doi.org/10.1126/sciadv.aaw5873openalex-snapshot
Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
inferredcites →https://doi.org/10.1126/science.1188021openalex-snapshot
A Draft Sequence of the Neandertal Genome
inferredcites →https://doi.org/10.1126/science.1216304openalex-snapshot
Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
inferredcites →https://doi.org/10.1126/science.aar7711openalex-snapshot
The first horse herders and the impact of early Bronze Age steppe expansions into Asia
inferredcites →https://doi.org/10.1146/annurev-genom-083117-021749openalex-snapshot
Ancient Genomics of Modern Humans: The First Decade
inferredcites →https://doi.org/10.1186/1471-2164-13-178openalex-snapshot
Improving ancient DNA read mapping against modern reference genomes
inferredcites →https://doi.org/10.1186/gb-2010-11-5-r47openalex-snapshot
Computational challenges in the analysis of ancient DNA
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1186/s12915-018-0581-9openalex-snapshot
Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
inferredcites →https://doi.org/10.1186/s13059-020-1935-5openalex-snapshot
Opportunities and challenges in long-read sequencing data analysis
inferredcites →https://doi.org/10.1186/s13104-016-1900-2openalex-snapshot
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1371/journal.pbio.0030339openalex-snapshot
The Geographic Spread of the CCR5 Δ32 HIV-Resistance Allele
inferredcites →https://doi.org/10.1371/journal.pbio.0030378openalex-snapshot
The Case for Selection at CCR5-Δ32
inferredcites →https://doi.org/10.1371/journal.pgen.0020190openalex-snapshot
Population Structure and Eigenanalysis
inferredcites →https://doi.org/10.1371/journal.pgen.1008302openalex-snapshot
The presence and impact of reference bias on population genomic studies of prehistoric human populations
inferredcites →https://doi.org/10.1534/genetics.112.145037openalex-snapshot
Ancient Admixture in Human History

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/evl3.165openalex-snapshot
Inference of natural selection from ancient DNA
inferred← citeshttps://doi.org/10.1007/978-3-030-86258-9_11openalex-snapshot
A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping
inferred← citeshttps://doi.org/10.1099/mgen.0.000437openalex-snapshot
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
inferred← citeshttps://doi.org/10.1101/2020.06.22.164186openalex-snapshot
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
inferred← citeshttps://doi.org/10.1111/mec.16113openalex-snapshot
Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species
inferred← citeshttps://doi.org/10.1186/s13059-020-02229-3openalex-snapshot
Reference flow: reducing reference bias using multiple population genomes
inferred← citeshttps://doi.org/10.1186/s13059-021-02442-8openalex-snapshot
VariantStore: an index for large-scale genomic variant search
inferred← citeshttps://doi.org/10.1186/s13059-024-03240-8openalex-snapshot
Measuring, visualizing, and diagnosing reference bias with biastools
inferred← citeshttps://doi.org/10.3389/fevo.2020.00105openalex-snapshot
Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes
inferred← citeshttps://doi.org/10.70675/afd704b6z444cz4392z8f50z1695fba1c117openalex-snapshot
Epigenomic study on the domestication of the horse using ancient DNA
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