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Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale

Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale

Authors :
Bin Hu
Shane Canon
Emiley A. Eloe-Fadrosh
Anubhav
Michal Babinski
Yuri Corilo
Karen Davenport
William D. Duncan
Kjiersten Fagnan
Mark Flynn
Brian Foster
David Hays
Marcel Huntemann
Elais K. Player Jackson
Julia Kelliher
Po-E. Li
Chien-Chi Lo
Douglas Mans
Lee Ann McCue
Nigel Mouncey
Christopher J. Mungall
Paul D. Piehowski
Samuel O. Purvine
Montana Smith
Neha Jacob Varghese
Donald Winston
Yan Xu
Patrick S. G. Chain
Source :
Frontiers in Bioinformatics, Vol 1 (2022)
Publication Year :
2022
Publisher :
Frontiers Media S.A., 2022.

Abstract

The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.

Details

Language :
English
ISSN :
26737647
Volume :
1
Database :
Directory of Open Access Journals
Journal :
Frontiers in Bioinformatics
Publication Type :
Academic Journal
Accession number :
edsdoj.6956a6b3c54bc0a65af4d854b974d9
Document Type :
article
Full Text :
https://doi.org/10.3389/fbinf.2021.826370