Mapache: a flexible pipeline to map ancient DNA.

ABSTRACT:

Summary

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.

Availability and implementation

Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Neuenschwander S 

PROVIDER: S-EPMC9901408 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature