| Title: |
Mapache:a flexible pipeline to map ancient DNA |
| Authors: |
Neuenschwander, Samuel; Cruz Dávalos, Diana I; Anchieri, Lucas; Sousa da Mota, Bárbara; Bozzi, Davide; Rubinacci, Simone; Delaneau, Olivier; Rasmussen, Simon; Malaspinas, Anna-Sapfo |
| Source: |
Neuenschwander , S , Cruz Dávalos , D I , Anchieri , L , Sousa da Mota , B , Bozzi , D , Rubinacci , S , Delaneau , O , Rasmussen , S & Malaspinas , A-S 2023 , ' Mapache : a flexible pipeline to map ancient DNA ' , Bioinformatics (Online) , vol. 39 , no. 2 . https://doi.org/10.1093/bioinformatics/btad028 |
| Publication Year: |
2023 |
| Collection: |
University of Copenhagen: Research / Forskning ved Københavns Universitet |
| Subject Terms: |
Software; DNA; Ancient; Genome; Workflow |
| Description: |
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. |
| Document Type: |
article in journal/newspaper |
| File Description: |
application/pdf |
| Language: |
English |
| DOI: |
10.1093/bioinformatics/btad028 |
| Availability: |
https://researchprofiles.ku.dk/da/publications/cc050f2f-ebf2-4452-8879-3db07f40c397; https://doi.org/10.1093/bioinformatics/btad028; https://curis.ku.dk/ws/files/351114886/btad028.pdf |
| Rights: |
info:eu-repo/semantics/openAccess |
| Accession Number: |
edsbas.29D2799 |
| Database: |
BASE |