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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.
Afiliação
  • Neuenschwander S; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.
  • Cruz Dávalos DI; Vital-IT, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
  • Anchieri L; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.
  • Sousa da Mota B; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
  • Bozzi D; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.
  • Rubinacci S; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
  • Delaneau O; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.
  • Rasmussen S; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
  • Malaspinas AS; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.
Bioinformatics ; 39(2)2023 02 03.
Article em En | MEDLINE | ID: mdl-36637197
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.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / DNA Antigo Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Suíça

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / DNA Antigo Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Suíça