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.