Thang, Mike W. C., Chua, Xin-Yi, Price, Gareth, Gorse, Dominique, and Field, Matt A. (2019) MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data [version 2; peer review: 2 approved]. F1000Research, 8. 726.

Preview

PDF (Published version) - Published Version Available under License Creative Commons Attribution. Download (2MB) | Preview

Abstract

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results.

Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files.

Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

Item ID:	60907
Item Type:	Article (Research - C1)
ISSN:	2046-1402
Keywords:	Galaxy, metagenomics, differential abundance, high throughput sequencing, phyloseq
Copyright Information:	© 2019 Thang MWC et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) License.
Funders:	James Cook University
Date Deposited:	25 Nov 2019 02:13
FoR Codes:	31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310201 Bioinformatic methods development @ 50% 31 BIOLOGICAL SCIENCES > 3107 Microbiology > 310704 Microbial genetics @ 50%
SEO Codes:	89 INFORMATION AND COMMUNICATION SERVICES > 8902 Computer Software and Services > 890201 Application Software Packages (excl. Computer Games) @ 100%
Downloads:	Total: 238 Last 12 Months: 13
	More Statistics