MGnify Visualization Recon
Sample Viz
Map of sample locations
Example URL: https://www.ebi.ac.uk/metagenomics/studies/MGYS00001606#overview
What it shows: Location of the samples collected
Dataset: Sample metadata (from ENA)
Visualization type: Geographical Map
Technology used: Google Maps embed
Analysis Viz
Quality Control
Example URL: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00584637#qc
Technology used: Highcharts
Dataset: Accessed through Analyses Accession ID - Summary
Number of Sequence Reads per QC step
What it shows: Number of reads which pass the quality control steps in the pipeline.
Visualization type: Normal X-axis Charts
Read Length & Read GC Distribution
What it shows: Histograms showing distributions of sequence lengths and percentage GC content for the sequences having passed quality control.
Visualization type: Histogram
Nucleotide Position Histogram
What it shows: Shows the relative abundance of nucleotides (A, C, G, T, or ambiguous base "N") at each position starting from the beginning of each read up to the first 500 base pairs.
Visualization type: Histogram
Dataset: Accessed through Analyses Accession ID - nucleotide-distribution
Taxonomic analysis
Results from the taxonomic analysis steps of the pipeline.
Example URL: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00584637#taxonomic
Krona
What it shows: Interactive Krona to visualise the taxa hierarchy
Technology used: https://github.com/marbl/Krona/wiki
Visualization type: Krona
Dataset: Accessed through Analyses Accession ID - krona${taxResults}
Domain Composition
Technology used: Highcharts
Visualization type: Pie, Column
Dataset: Accessed through Analysis Accession ID - taxonomy
Phylum Composition
Technology used: Highcharts
Visualization type: Pie, Column, Stacked Column
Dataset: Accessed through Analysis Accession ID - taxonomy
Functional analysis
Charts present the functional analysis outputs of the pipeline, which focus on InterPro, Pfam, KEGG orthologue and GO term annotations. These summarise the functional content of the sequences in the sample.
Example URL: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00584637#functional
InterPro
What it shows: Shows Sequence feature summary & InterPro Summary
Technology used: Highcharts
Visualization type: X-axis Chart, Pie
GO Terms
What it shows: A summary of Gene Ontology (GO) terms derived from InterPro matches to the sample is provided in the charts below.
Technology used: Highcharts
Visualization type: Bar, Pie
Pfam
What it shows: Top 10 Pfam entries
Technology used: Highcharts
Visualization type: Bar
KO
What it shows: Top 10 KO entries
Technology used: Highcharts
Visualization type: Bar
Contig Viewer
What it shows: Contig browser for the assembly contigs
Dataset: through assembly ID, FASTA URL
Visualization type: Contig viewer
Technology used: IGV
Pathways/Systems
Results from the biochemical pathways and systems predictions steps of the pipeline.
Example URL: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00572069#path-systems
KEGG Module
What it shows: Modules vs Completeness
Dataset: analyses/${overviewData.id}/kegg-modules
Visualization type: Bar Chart
Technology used: Highcharts
Genome properties
What it shows: Hierarchical structure of Genome Properties
Dataset: analyses/${overviewData.id}/genome-properties
Visualization type: Hierarchy tree
Technology used: HierarchyNode
antiSMASH
What it shows: Displays top 10 antiSMASH gene clusters
Dataset: analyses/${overviewData.id}/antismash-gene-clusters
Visualization type: Bar Chart
Technology used: Highcharts
Genome Viz
Example URL: https://www.ebi.ac.uk/metagenomics/genomes/MGYG000320984#genome-browser
Browse genome
What it shows: A container with IGV genome browser, also allows selection of feature types
Dataset: General feature format : ${accession}.gff, fasta : ${accession}.fna
Visualization type: Genome browser + Functional Annotation
Technology used: IGV
COG Analysis
What it shows: Displays Top 10 COG Categories
Dataset: ${accession}/cogs
Visualization type: Bar Chart
Technology used: Highcharts
KEGG Class Analysis
What it shows: Displays Top 10 KEGG brite Categories
Dataset: ${accession}/kegg-class
Visualization type: Bar Chart
Technology used: Highcharts
KEGG Module Analysis
What it shows: Displays Top 10 KEGG module Categories
Dataset: ${accession}/kegg-module
Visualization type: Bar Chart
Technology used: Highcharts
Taxonomy Tree
Example URL: https://www.ebi.ac.uk/metagenomics/genome-catalogues/chicken-gut-v1-0#phylo-tab
What it shows: Phylogenetic Tree
Dataset: phylo_tree.json
Visualization type: HierarchyNode
Kegg pathway Visualization
Example URL: https://github.com/EBI-Metagenomics/notebooks/blob/pathways_vis/src/notebooks/R%20Examples/pathways_vis.ipynb (not yet live)
What it shows: completeness of KEGG pathways for a sample
Dataset: combination of an MGYA Kegg Module list and a Pathway from KEGG API
Visualization type: pathway network
Technology used: pathview R package