ANALYSIS WORFLOW
1
Introduction
1.1
Prepare the R environment
1.2
Download mock data
2
Data summary
2.1
Load the data
2.2
General data statistics
Number of samples
Amount of discarded data
Amount of host data
Amount of metagenomic data
Amount of estimated prokaryotic
2.3
General MAG statistics
Number of MAGs
Number of MAGs without species-level annotation
2.3.1
Number of phylums
2.4
Geographic distribution
2.5
Prepare the colour layout
3
MAG catalogue
3.1
MAG phylogeny
Prepare MAG metadata
Plot phylogenetic tree
Plot phylum color legend
3.2
MAG quality
Prepare input table
Create biplot chart
Create boxplot charts
Create composite figure
3.3
Functional attributes of MAGs
3.4
Functional ordination of MAGs
4
Sequencing Assessment
4.1
DNA fractions
4.2
Estimated vs. mapped prokaryotic fraction
4.3
Additional sequencing needed
5
Count data
5.1
Minimum coverage filtering
5.2
Genome size normalisation
5.3
Count table
6
Taxonomic composition
6.1
Taxonomy stacked barplot
7
Diversity analyses
7.1
Data preparation
7.2
Alpha diversity
Alpha diversity metrics
Alpha diversity plots
Alpha diversity comparisons
Relationship between alpha diversity and sequencing effort
7.3
Beta diversity
Beta diversity test
Beta diversity plot
References
Earth Hologenome Initiative
Laboratory workflow
Bioinformatics workflow
The Earth Hologenome Initiative Data Analysis Workflow
References