MetaDEGalaxy

MetaDEGalaxy is a metagenomic analysis tool running on Galaxy platform. There is a number of scripts written in R and python to make up the Galaxy workflow to perform 16S rRNA analysis. The greengenes database is used as a reference database in the MetaDEGalaxy.

References

Mike W. C. Thang, X. Chua, G. Price, Dominique Gorse, Matthew A Field, 2019. Metadegalaxy: Galaxy Workflow For Differential Abundance Analysis Of 16S Metagenomic Data.

Tool

• PEAR - Paired-End reAd mergeR
• VSEARCH - It is an alternative to the USEARCH tool

Script dependencies:

• Biopython (v 1.74)
• python >=3
• Bioconductor-phyloseq (v 1.22.3)
• r-base (v 3.4.1)
• r-getopt (v 1.20.0)
• ghostscript (v 9.18)
• bioconductor-deseq2 (v 1.18.1)
• r-data.table (v 1.10.0)

Script

• uc2otutable - a python script to transform UC file format to tabular format. Note: UC file format
• pear_stats - a python script to generate an overlapping statistic report using the log file generated by PEAR.
• reheader - a python script to rename the read identifier by appending the sample name to end of the read identifier.
• phyloseq_richness - a R package phyloseq is used to generate richness plot.
• phyloseq_abundance_taxonomy - a script using R package phyloseq to generata abundance plot by taxonomy.
• phyloseq_abundance_factor - a script R using package phyloseq to generate abundance plot by factor.
• phyloseq_2_deseq2 - a script using R package phyloseq and DESeq2 to generate differential abundance count table.
• phyloseq_net - a script using R package phyloseq to generate network plot based on the sample distance matrix.
• symmetric_plot - using ggplot2 to generate a symmetric plot

Ansible script

This ansible script contains all the tools, scripts and Galaxy wrappers for MetaDeGalaxy. It can be used to install on a Galaxy Instance ( GVL 4.1.0 / ubuntu 14.04). More informatin can be found here.

Data

The testing data for MetaDEGalaxy is obtained from mothur website. More information about the dataset can be found on the mothur MiSeq SOP Getting started section.

Tutorial

• Galaxy workflow tutorial can be found here

Additional python script

One of the python scripts are obtained from USearch. The script uc2otutable.py was modified to run in python3 environment.