A fully reproducible and state-of-the-art ancient DNA analysis pipeline

A tool to infer metagenomic sample composition

This repository contains practical data analyses exercises for the special course on Paleogenomics and Anthropology held at the National School of Anthropology of Mexico (ENAH), May 6 to 10, 2019. Topics include performing QC on aDNA NGS data, assigning mtDNA haplogroups and testing hypotheses w/PCA and ADMIXTURE analyses. No previous command-li…

🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

Perl scripts for reconstructing the structure of double-stranded DNA fragments from single-stranded DNA libraries

Script and utilities applied to perform kinship analysis between ancient Mentesh-Tepe individuals, found in (Garino-Vignon, P., et al 2023)

Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)

Perform hard selective masking of ancient DNA deamination patterns, using the output misincorporation frequency estimates of MapDamage (https://ginolhac.github.io/mapDamage/)

A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods