TaxSEA
BioconductorTaxon set enrichment analysis. Turn a ranked list of differentially abundant taxa into interpretable signatures from BugSigDB, MiMeDB and other curated databases in seconds.
BiocManager::install("TaxSEA")Software & methods
Open-source tools for microbiome analysis, and the benchmarks and best-practice guidance behind them. Bug reports and feature requests are welcome on GitHub.
OpusTaxa
SnakemakeOne workflow from raw shotgun reads to results: QC, host removal, taxonomic profiling, assembly and functional annotation, locally or on SLURM clusters.
- fastp
- FastQC
- MultiQC
- Nonpareil
- MetaPhlAn
- Kraken2
- Bracken
- SingleM
Best practice
Pitfalls in human metagenomic analyses
The common traps in human metagenome studies, from sparse and low-prevalence taxa to reproducibility, and how to avoid them. Illustrated with public stool metagenomes, with all analysis code available.
More tools & best practice
FMTrace
R · 2026Compositional barplots of faecal microbiota transplantation donors and recipients, with each species coloured by where it was detected. A quick species-level screen for possible donor-to-recipient transmission.
SPINGO
Python · 2015Rapid species-level classifier for 16S rRNA amplicon sequences, developed with Guy Allard and Marcus Claesson at University College Cork.
Metagenomics tools atlas
ResourceA curated inventory of tools and resources for short-read shotgun metagenomics.
Choice of assembly software has a critical impact on virome characterisation
Microbiome 2019A benchmark showing that the assembler you pick changes which viruses you find, and by how much.
Reproducible protocols for metagenomic analysis of human faecal phageomes
Microbiome 2018Laboratory and computational protocols for consistent, comparable studies of the bacteriophages in human stool.