YAMP: a containerized workflow enabling reproducibility in metagenomics research

YAMP ("Yet Another Metagenomics Pipeline") is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system and of...

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Detalles Bibliográficos
Autores principales: Visconti, Alessia, Martin, Tiphaine C, Falchi, Mario
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Technical Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047416/
https://www.ncbi.nlm.nih.gov/pubmed/29917068
http://dx.doi.org/10.1093/gigascience/giy072
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author Visconti, Alessia
Martin, Tiphaine C
Falchi, Mario
author_facet Visconti, Alessia
Martin, Tiphaine C
Falchi, Mario
author_sort Visconti, Alessia
collection PubMed
description YAMP ("Yet Another Metagenomics Pipeline") is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. Although YAMP was developed to be ready to use by nonexperts, bioinformaticians will appreciate its flexibility, modularization, and simple customization.
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spelling pubmed-60474162018-07-19 YAMP: a containerized workflow enabling reproducibility in metagenomics research Visconti, Alessia Martin, Tiphaine C Falchi, Mario Gigascience Technical Note YAMP ("Yet Another Metagenomics Pipeline") is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. Although YAMP was developed to be ready to use by nonexperts, bioinformaticians will appreciate its flexibility, modularization, and simple customization. Oxford University Press 2018-06-18 /pmc/articles/PMC6047416/ /pubmed/29917068 http://dx.doi.org/10.1093/gigascience/giy072 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
Visconti, Alessia
Martin, Tiphaine C
Falchi, Mario
YAMP: a containerized workflow enabling reproducibility in metagenomics research
title YAMP: a containerized workflow enabling reproducibility in metagenomics research
title_full YAMP: a containerized workflow enabling reproducibility in metagenomics research
title_fullStr YAMP: a containerized workflow enabling reproducibility in metagenomics research
title_full_unstemmed YAMP: a containerized workflow enabling reproducibility in metagenomics research
title_short YAMP: a containerized workflow enabling reproducibility in metagenomics research
title_sort yamp: a containerized workflow enabling reproducibility in metagenomics research
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047416/
https://www.ncbi.nlm.nih.gov/pubmed/29917068
http://dx.doi.org/10.1093/gigascience/giy072
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