Mapache: a flexible pipeline to map ancient DNA
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Mapache : a flexible pipeline to map ancient DNA. / Neuenschwander, Samuel; Cruz Dávalos, Diana I; Anchieri, Lucas; Sousa da Mota, Bárbara; Bozzi, Davide; Rubinacci, Simone; Delaneau, Olivier; Rasmussen, Simon; Malaspinas, Anna-Sapfo.
I: Bioinformatics (Online), Bind 39, Nr. 2, 2023.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Mapache
T2 - a flexible pipeline to map ancient DNA
AU - Neuenschwander, Samuel
AU - Cruz Dávalos, Diana I
AU - Anchieri, Lucas
AU - Sousa da Mota, Bárbara
AU - Bozzi, Davide
AU - Rubinacci, Simone
AU - Delaneau, Olivier
AU - Rasmussen, Simon
AU - Malaspinas, Anna-Sapfo
N1 - © The Author(s) 2023. Published by Oxford University Press.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - Software
KW - DNA, Ancient
KW - Genome
KW - Workflow
U2 - 10.1093/bioinformatics/btad028
DO - 10.1093/bioinformatics/btad028
M3 - Journal article
C2 - 36637197
VL - 39
JO - Bioinformatics (Online)
JF - Bioinformatics (Online)
SN - 1367-4811
IS - 2
ER -
ID: 346589617