ArticleBioinformatics (Oxford, England)2017
gargammel: a sequence simulator for ancient DNA.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- Co-mutation Based Genetic Networks to Infer Temporal Mutation Dynamics in Ancient Human Mitochondrial Genomes.Journal of molecular evolution · 2026Article
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- Molecular Clock Dating of Ancient Environmental DNA Reveals Damage Beyond Deamination.bioRxiv : the preprint server for biology · 2026Article
- Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years.Nature communications · 2026Article
- FALCON2: compression-based metagenomic classification of ancient viruses.Bioinformatics (Oxford, England) · 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
- sedimix: a workflow for the analysis of hominin nuclear DNA sequences from sediments.Bioinformatics (Oxford, England) · 2026Article
- Mapping the Genomic Limits of De-Extinction in the Face of Ancient DNA Degradation.Genome biology and evolution · 2026Article
- How low can you go? Establishing detection limits for rare eukaryotes in Southern Ocean sedimentary ancient DNA.Bioinformatics advances · 2026Article
- Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.Frontiers in microbiology · 2026Article
- EGGS: Empirical Genotype Generalizer for Samples.Bioinformatics advances · 2026Article
- Palaeogenomics suggest domesticated camelid herding and wild camelid hunting in early pastoralist societies in the Atacama Desert.Nature communications · 2025Article
- Quick Analysis of Sedimentary Ancient DNA Using quicksand.Molecular biology and evolution · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets.Genome biology · 2025Article
- Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.G3 (Bethesda, Md.) · 2025Article
- Article
- Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic.Scientific reports · 2025Article
- Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads.Molecular biology and evolution · 2025Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico , we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets. Availability and Implementation: The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL. Contact: gabriel.renaud@snm.ku.dk. Supplementary information: Supplementary data are available at Bioinformatics online.
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