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. 2017 Aug 1;6(8):1-11.
doi: 10.1093/gigascience/gix047.

The metagenomic data life-cycle: standards and best practices

Petra Ten Hoopen  1 , Robert D Finn  1 , Lars Ailo Bongo  2 , Erwan Corre  3 , Bruno Fosso  4 , Folker Meyer  5 , Alex Mitchell  1 , Eric Pelletier  6   7   8 , Graziano Pesole  4   9 , Monica Santamaria  4 , Nils Peder Willassen  2 , Guy Cochrane  1
Affiliations

The metagenomic data life-cycle: standards and best practices

Petra Ten Hoopen et al. Gigascience. .

Abstract

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.

Keywords: best practice; data analysis; metadata; metagenomics; sampling; sequencing; standard.

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Figures

Figure 1:
Figure 1:
A generalized metagenomics data analysis workflow in the context of other “omics” approaches.
Figure 2:
Figure 2:
A common data model for read data and associated metadata.
Figure 3:
Figure 3:
Schematic overview of best practice for analysis metadata collection with example fields. A) Overarching metadata; B) Analysis component; C) Workflow.
See this image and copyright information in PMC

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