Below is a list of specialised set of microbial genomics-focussed analysis and visualisation tools that will be integrated into the Galaxy platform under this project. These will provide the initial functionality required for primary/secondary analysis of genomics and transcriptomics data, assembly of microbial genomes using the distributed PacBio SmrtPortal tool suite, annotation of assembled genomes, and visualisation of the annotated genomes and differential gene expression analyses. This managed Microbial GVL is available at http://abrpi.genome.edu.au

Function Incorporated/Connected Planned
Genomics Assembly, Mapping SPAdes, HGAP3 (SMRT), BWA-MEM, Bowtie2
Variant Calling Snippy Pilon
Genome Annotation Prokka, WebApollo
Transcriptomics Read Counts, Gene Expression Htseq-count, DESeq2, Voom, DeGust  EdgeR
Proteomics Protein Identification X!tandem, Limma
Metabolomics Metabolite Identification XCMS, R package (MA)
Metabolic Pathway Analysis MetaCyc/BioCyc, Pathway Tools
Visualisation Phylogenetics Trees FastTree RAxML
Genome Browsers IGV, JBrowse
Metabolic Pathway Visualisation Pathway Tools
Multi-Omics Integrative Analysis Overlay of multi-omics data on metabolic pathways MetaCyc/BioCyc, Pathway Tools
Statistical integration of multi-omics data MixOmics R package