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This repository contains all computational analyses used in my 2020 paper “The evolutionary history of Neandertal and Denisovan Y chromosomes”.

Contents

You can find here:

  • my complete data processing and data-generation pipeline - processing of BAM files, genotype calling, simulations etc. (Makefile);
  • scripts used by the Makefile pipeline (src/) and R functions used for analyses (R/);
  • R Jupyter notebooks used to generate every result in the paper (notebooks/);
  • cached results in the rds format - useful for re-producing all tables and figures in the paper without having to first re-process sequencing data or run SLiM simulations (data/rds/); for full data access see here.

Note that the repository is structured as an R package, with the exception that it contains not only the required R package components (R code in R/, the DESCRIPTION file etc.), but also the data and analyses themselves. Therefore, after cloning this repository, you can simply call devtools::load_all(".") from the root of the repository in an R console and immediately start exploring the data yourself.

All software dependencies used in the project are described in detail in this notebook.

Data availability

In addition to cached results in data/rds in this repository, all sequencing data (BAM/VCF/FASTA files), raw simulation outputs, as well as the sequences of capture probes can be found at: https://bioinf.eva.mpg.de/archaic-ychr.

Contact

In case of trouble, please don’t hesitate to contact me or Janet Kelso.

License

All software (bash/R/Python scripts) are available under MIT license. The contents of Jupyter notebooks (which include text, figures, tables etc.) and other non-software files in this repository are available under CC BY 4.0 license.

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Repository of code for the paper "The evolutionary history of Neandertal and Denisovan Y chromosomes" by Petr et al.

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