lefse

name	lefse
description	LEfSe — Linear discriminant analysis Effect Size for metagenomic biomarker discovery between classes (taxa, genes, pathways). Use for classic LDA-style biomarkers and cladograms; prefer MaAsLin2/3 when many covariates or longitudinal designs are required. Upstream: https://github.com/SegataLab/lefse · bioBakery docs. Route via research-analysis.
license	MIT
category	evaluation
tags	["LEfSe","biomarker","LDA","differential-abundance","bioBakery"]
upstream	https://github.com/SegataLab/lefse
stage	report

LEfSe

Upstream: SegataLab/lefse · https://huttenhower.sph.harvard.edu/lefse/

Citation

Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011). https://doi.org/10.1186/gb-2011-12-6-r60

See also docs/references.md.

Analytical thinking

LEfSe couples nonparametric tests with LDA effect size and (optionally) cladogram displays — widely used in papers but sensitive to compositionality and limited for complex multivariable designs. Prefer maaslin2 for modern covariate-adjusted analyses; LEfSe remains useful for simple class contrasts and familiar LDA plots.

Pin LDA cutoff, multiclass strategy, and input table type (relative abundances).

How to run

# conda install -c bioconda lefse   # or biobakery channel — verify
# format input table per Galaxy/tutorial (class + subclass rows)
# lefse_format_input.py … ; run_lefse.py … ; lefse_plot_*.py …

Follow the installed bioBakery tutorial for exact script names.

Decision tree

Biomarker discovery?
├─ Simple classes / LDA plots → lefse
├─ Covariates / mixed models → maaslin2
└─ Broad exploration → microeco

Related skills

research-analysis · maaslin2 · microeco · visualization · metaphlan · humann · tool-selection