Mapache: a flexible pipeline to map ancient DNA

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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.

In: Bioinformatics (Online), Vol. 39, No. 2, 2023.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Neuenschwander, S, Cruz Dávalos, DI, 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

APA

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), 39(2). https://doi.org/10.1093/bioinformatics/btad028

Vancouver

Neuenschwander S, Cruz Dávalos DI, Anchieri L, Sousa da Mota B, Bozzi D, Rubinacci S et al. Mapache: a flexible pipeline to map ancient DNA. Bioinformatics (Online). 2023;39(2). https://doi.org/10.1093/bioinformatics/btad028

Author

Neuenschwander, Samuel ; Cruz Dávalos, Diana I ; Anchieri, Lucas ; Sousa da Mota, Bárbara ; Bozzi, Davide ; Rubinacci, Simone ; Delaneau, Olivier ; Rasmussen, Simon ; Malaspinas, Anna-Sapfo. / Mapache : a flexible pipeline to map ancient DNA. In: Bioinformatics (Online). 2023 ; Vol. 39, No. 2.

Bibtex

@article{cc050f2febf2445288793db07f40c397,
title = "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.",
keywords = "Software, DNA, Ancient, Genome, Workflow",
author = "Samuel Neuenschwander and {Cruz D{\'a}valos}, {Diana I} and Lucas Anchieri and {Sousa da Mota}, B{\'a}rbara and Davide Bozzi and Simone Rubinacci and Olivier Delaneau and Simon Rasmussen and Anna-Sapfo Malaspinas",
note = "{\textcopyright} The Author(s) 2023. Published by Oxford University Press.",
year = "2023",
doi = "10.1093/bioinformatics/btad028",
language = "English",
volume = "39",
journal = "Bioinformatics (Online)",
issn = "1367-4811",
publisher = "Oxford University Press",
number = "2",

}

RIS

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