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Modern and Ancient Genomes Group - Tools
Modern and Ancient Genomes Group

Tools & Education

Welcome to the ‘Tools and Education’ section!

At the Modern and Ancient Genomes Group, we develop software tools for ancient DNA, environmental DNA, sedimentary DNA, low-coverage data, NGS data and allele frequencies. Our tools are fully open-source and free to use.

Are you interested in improving your bioinformatics or population genetics skills? Then scroll down to the Education section, you will find courses at the Technical University of Denmark to do just that!

Tools

Software

safari

safari is an aligner to pangenomes built on top of “vg giraffe” that is robust to ancient DNA damage

CarpeDeam

CarpeDeam is an assembly algorithm for ancient metagenomics

soibean

soibean (part of vgan) is a tool for species identification that can handle mixtures and abundance estimation for ancient environmental DNA.

euka

euka (part of vgan) is a tool for bilaterian abundance estimation of ancient environmental DNA.

HaploCart

Haplocart (part of vgan) classifies modern human mtDNA haplogroup.

cinch

cinch is a non-negative matrix factorization tool to infer levels of tumor DNA from cell-free DNA.

ROHan

ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity. ROHan can work on modern and ancient samples with signs of ancient DNA damage.

gargammel

gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present-day human contamination and microbial contamination.

glactools

glactools is a set of command-line tools for the management of Genotype Likelihood (GL) and Allele Counts (AC).

DICE

DICE is a Bayesian method to jointly estimate error rates, demographic parameters and the rate of contamination from present-day humans in ancient DNA (aDNA) samples from modern or archaic humans. Our approach is based on an MCMC sampler, and is applicable to nuclear autosomal aDNA data. It can also serve to infer the most probable ancestry of the individual(s) that contaminated the sample.

Schmutzi

schmutzi is a set of programs aimed at ancient DNA data that can estimate contamination based on deamination patterns alone, call a mitochondrial consensus for the endogenous genome while taking into account contamination and deamination and estimate mitochondrial contamination and identify the most likely contaminant.

deML

deML is a program for maximum likelihood demultiplexing of next-generation sequencing data.

leeHom

leeHom is a program to trim adapters and merge overlapping sequencing using a Bayesian reconstruction. This is particularly useful for ancient DNA and or DNA with a short fragment size like cell-free DNA.

Educational resources

22126 - Introduction to Next-Generation Sequencing Analysis

Three-week graduate-level course on introduction to next-generation sequencing (NGS) data analysis, introduction to UNIX and command-line use.

Introduction to population genetics, human ancestry and health

Three-month graduate-level course to understand basic concepts in population genetics concepts and their links to human health and disease (starting Fall 2024)

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