Article,
Mapache: a flexible pipeline to map ancient DNA
Contributors
Neuenschwander, Samuel
0000-0002-4080-5546
(Corresponding author)
[1]
[2]
Rubinacci, Simone
0000-0002-7725-4813
[1]
[2]
Delaneau, Olivier
0000-0002-3906-8446
[1]
[2]
Rasmussen, Simon
0000-0001-6323-9041
[3]
Malaspinas, A.-s.
0000-0003-1001-7511
[1]
[2]
Affiliations
- [1] Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland [NORA names: Switzerland; Europe, Non-EU; OECD];
- [2] Univ Lausanne, Dept Computat Biol, CH-1015 Lausanne, Switzerland [NORA names: Switzerland; Europe, Non-EU; OECD];
- [3] Univ Copenhagen, Novo Nordisk Fdn Ctr Prot Res, DK-2200 Copenhagen, Denmark [NORA names: KU University of Copenhagen; University; Denmark; Europe, EU; Nordic; OECD]
Abstract
We introduce mapache, a flexible, robust and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large datasets-such as reference panels and multiple extracts and libraries per sample- to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.
