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. 2018 Jul 1;7(7):giy072.
doi: 10.1093/gigascience/giy072.

YAMP: a containerized workflow enabling reproducibility in metagenomics research

Alessia Visconti  1 , Tiphaine C Martin  1 , Mario Falchi  1
Affiliations

YAMP: a containerized workflow enabling reproducibility in metagenomics research

Alessia Visconti et al. Gigascience. .

Abstract

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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Figures

Figure 1:
Figure 1:
The YAMP workflow. White rectangles represent data to be provided as input, and blue rectangles those produced in output. Pentagons represent the analysis steps.
Figure 2:
Figure 2:
An excerpt from the YAMP execution log.
Figure 3:
Figure 3:
An example of the YAMP execution profile. YAMP returns the time spent during its complete execution and in each step, as well as the steps’ memory peaks.
Figure 4:
Figure 4:
Phylum-level relative abundances. Each vertical bar represents a sample. Phylum relative abundances were estimated by YAMP using MetaPhlAn2. Unspecified viral phyla are not shown.
See this image and copyright information in PMC

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