Key Points

Introduction to metagenomics

Metagenomics sequences all DNA, giving an unbiased, high-resolution view of community composition and function—beyond what amplicon sequencing can capture.
Reads profiling delivers fast, reference-based taxonomic and functional counts data for downstream analyses like TaxSEA and integration workflows.
MAGs can be reconstructed via assembly and binning of reads, revealing uncultured lineages and their metabolic potential.
Modern sequencing and workflows (short-reads, long-reads, hybrids; nf-core pipelines) improve accuracy, assembly quality, and reproducibility.

TaxSEA performs taxon-set enrichment analysis on differential abundance results, similar to GSEA.
Inputs must be species or genus names with corresponding ranks (e.g., log2 fold changes).
TaxSEA tests whether members of a taxon set are skewed toward one end of the ranked distribution.
Enrichment results help reveal functional or ecological patterns that may not be visible at the single-taxon level.

DIABLO integrates multiple omics datasets by identifying correlated and discriminative features across blocks.
Proper filtering and transformation of each omics dataset are essential for stable multi-omics models.
Tuning (components and keepX) guides the selection of the most predictive and biologically relevant features.
DIABLO visualisations (sample plots, arrow plots, circos, CIM) reveal relationships across omics and help interpret multi-omics signatures.