Résumé
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field. This resource will provide the foundations for those newly entering the microbiome field and will provide much-needed guidance and best practices to ensure that quality microbiome research is undertaken. All protocols, scripts, workflows, tutorials, and virtual images are freely available through the Microbiome Helper website (https://github.com/mlangill/microbiome-helper/wiki).
Langue d'origine | English |
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Numéro d'article | e00127 |
Journal | mSystems |
Volume | 2 |
Numéro de publication | 1 |
DOI | |
Statut de publication | Published - janv. 1 2017 |
Note bibliographique
Publisher Copyright:Copyright © 2017 Comeau et al.
ASJC Scopus Subject Areas
- Microbiology
- Ecology, Evolution, Behavior and Systematics
- Biochemistry
- Physiology
- Modelling and Simulation
- Molecular Biology
- Genetics
- Computer Science Applications