Quick start

If you have bacterial or archaeal genomes — isolates or MAGs — that you want to analyze and compare, CompareM2 is the tool for you.

1) Install

With pixi on a Linux machine:

pixi global install -c conda-forge -c bioconda comparem2

2) Run

CompareM2 includes many analysis tools (full list). To run only the fast ones:

comparem2 --config input_genomes="path/to/my/genomes_*.fna" --until fast

3) Explore

When CompareM2 finishes, open the report in your browser:

results_comparem2/report_<title>.html

This dynamic HTML report summarizes the most important results from each analysis. See a demo report.

The full results are organized in results_comparem2/:

tree results_comparem2/ -L 1
#> results_comparem2/
#> ├── amrfinder/
#> ├── assembly-stats/
#> ├── benchmarks/
#> ├── checkm2/
#> ├── fasttree/
#> ├── gtdbtk/
#> ├── iqtree/
#> ├── kegg_pathway/
#> ├── mashtree/
#> ├── metadata.tsv
#> ├── mlst/
#> ├── panaroo/
#> ├── report_<title>.html
#> ├── samples/
#> │  └── <sample>/
#> │     ├── antismash/
#> │     ├── bakta/
#> │     ├── dbcan/
#> │     ├── eggnog/
#> │     ├── <sample>.fna
#> │     ├── interproscan/
#> │     ├── prokka/
#> │     └── sequence_lengths/
#> ├── snp-dists/
#> ├── visuals/
#> ├── treecluster/
#> └── version_info.txt

To run the full pipeline, simply omit the --until parameter.

If you have any problems, please file an issue: github.com/cmkobel/CompareM2/issues.