Data
- Genotype files for the 20 ancient African genomes generated in Wang et al. 2020
- BAM files of the 10 ancient British genomes generated in Schiffels et al. 2016
- BAM files of the three individuals with genome-wide data analysed in Schuenemann et al. 2017
- Genotype data of the present-day Siberian individuals described in Flegontov et al. 2019
- BAM Files for the ancient individuals described in Gretzinger et al. 2022.
Teaching Material
Disclaimer: These courses are currently not designed to “just work” if you run them at home. They are dependent on data that I provided to workshop participants at the time, and specific softare to be installed. Nevertheless, they may provide useful resources for some readers even outside of the original teaching context, that’s why I’m posting them here.
- May 2019: Six-hour practical course on “Computational Population Genetics” at the University of Jena, Germany, see https://github.com/stschiff/popgen_course
- January 22-24, 2019: Workshop on “Computational Population Genetics” at the MPI-SHH in Jena, Germany, see https://comppopgenworkshop2019.readthedocs.io/en/latest/
- December 12, 2018: Webinar with the student council of the Turkish regional group of the International Society for Computational Biology, Regional Group in Turkey: Link to Youtube-Video
- November 2018: Workshop on “Computational Methods to Analyse Human Genetic Variation”, see https://compvar-workshop.readthedocs.io/en/latest/
- May 2016: Workshop on Analysis of Genomic data. See https://gaworkshop.readthedocs.io/en/latest/
Software
All of my software can be found on github. For issues and discussions, please use the respective issues tracker, for example here for questions related to MSMC2.
Poseidon
Poseidon is a large initiative that is under development. We are preparing a public release soon
MSMC2
A method for analysing multiple genome sequences to infer past population sizes and separation history between populations. A utilities framework msmc-tools is available as well. Written in D and python.
Rarecoal
A method to model population graphs from the rare site frequency spectrum in multiple populations with large numbers of samples. A utilities package rarecoal-tools is available as well. Written in Haskell.
SequenceTools
This package contains two programs “pileupCaller” and “vcf2eigenstrat”. PileupCaller is used to sample alleles from an alignment file at a set of positions. VCF2eigenstrat converts a VCF file into eigenstrat format. Written in Haskell.