ATLAS and the ATLAS-pipeline

ATLAS, the Analysis Tools for Low-depth and Ancient Samples, are a suite of bioinformatic tools that cover all steps to gain insights from low-depth samples, including ancient samples. It learns and accounts for sequencing errors as well as post-mortem damage to calauclate accurate genotype likelihoods. These are then used to obtain variant calls, estimate genetic diversity of both individuals and populations, or to generate input files for a wide range of downstream analyses. It further offers a large suite of tools to process, diagnose and summarize sequencing data.

ATLAS is most easily used on batches of samples via the ATLAS-pipeline, a snakemake pipeline built around ATLAS.

Contributors

ATLAS and the ATLAS-pipeline are highly collaborative projects driven passionately by:

  • Andreas Füglistaler (current lead developer ATLAS)
  • Vivian Link (former lead developer ATLAS)
  • Athanasios Kousathanas (former lead developer ATLAS)
  • Xenia Wietlisbach (lead developer ATLAS-pipeline, contributor to ATLAS)
  • Ilektra Schulz (former lead developer ATLAS-pipeline, contributor to ATLAS)
  • Daniel Wegmann (initial developer, project lead)
  • Carlos Reyna (contributor)
  • Raphael Eckel (contributor)
  • Madleina Caduff (contributor)
  • Michael Jopiti (contributor)
  • Marc-Olivier Beausoleil (contributor)
  • Zuzana Hofmanova (contributor)
  • Jens Blöcher (testing & conceptual input)
  • Christoph Leuenberger (methodological input)
  • Krishna Veeramah (conceptual input)
  • Joachim Burger (conceptual input)
  • Aparna Pandey (documentation)
  • Kamil S Jaroň (bug fixes)
  • Christian Sell (testing)
  • Amelie Scheu (testing)

Citation

A paper describing ATLAS in detail is currently in the works. In the meantime, please cite our (unfortunately a bit dated) preprint:

ATLAS: Analysis Tools for Low-depth and Ancient Samples Vivian Link, Athanasios Kousathanas, Krishna Veeramah, Christian Sell, Amelie Scheu, Daniel Wegmann. bioRxiv 105346; doi: https://doi.org/10.1101/105346

If you make use of the ATLAS-pipeline, please cite the following paper:

The genomic origins of the world’s first farmers Marchi Nina, Laura Winkelbach, Ilektra Schulz, Maxime Barmi et al. Cell 185(11) doi: 10.1016/j.cell.2022.04.008