Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods
OPEN ACCESS
Author / Producer
Date
2020
Publication Type
Review Article
ETH Bibliography
yes
Citations
Altmetric
OPEN ACCESS
Data
Abstract
Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and function), the effective study of microbiomes (microbiomics) relies on the development, optimization, and validation of computational methods for analyzing microbial datasets, such as from marker-gene (e.g., 16S rRNA gene) and metagenome data. This review describes best practices for benchmarking and implementing computational methods (and software) for studying microbiomes, with particular focus on unique characteristics of microbiomes and microbiomics data that should be taken into account when designing and testing microbiomics methods.
Permanent link
Publication status
published
External links
Editor
Book title
Journal / series
Volume
18
Pages / Article No.
4048 - 4062
Publisher
Elsevier
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
Microbiome; Benchmarking; Software Development; Best practices; Metagenomics; Amplicon sequencing; Marker-gene sequencing
Organisational unit
09714 - Bokulich, Nicholas / Bokulich, Nicholas