BinBencher

BinBencher is a command-line interface (CLI) tool to evaluate metagenomic binnings given a ground-truth reference. It is the CLI version of the Julia library BinBencherBackend.jl. For more customised, flexible analysis of binnings, it may be preferred to use the backend directly in e.g. an interactive notebook.

Read the documentation on the BinBencherBackend.jl doc page

Quickstart

$ # Make a reference JSON file
$ binbench  binbench makeref ref_outdir --seq-mapping seq_mapping.tsv --seq-fasta contigs.fna \
--genome-directories organism=genomes --tax tax.tsv --tax-ncbi ncbi_out.tsv

$ # Benchmark using the reference and a binning TSV file.
$ binbench bench bench_outdir ref_outdir/reference.json binning.tsv

Installation of the CLI program

1. Install the Julia programming language
2. Launch the Julia REPL from a terminal by typing $ julia
3. Enter Pkg mode in the REPL by typing ]. You will see the prompt change from julia> to e.g. (@v1.12) pkg> depending on the Julia version.
4. Create a new globally accessible project (i.e. virtual environment) by typing activate @binbencher in the pkg REPL.
5. Add BinBencher to the environment with add https://github.com/jakobnissen/BinBencher.jl
6. In the pkg repl, type build

You will now have an executable script called binbench in the bin subdirectory your Julia home directory, e.g. on my computer it's at /home/jakni/.julia/bin/binbench. Add the bin folder to your PATH environmental variable to be able run to BinBencher as binbench from the shell.

Note

These installation instruction are convoluted, because, as of September 2024, Julia does not have a concept of installable applications. There is recent work to improve this, so hopefully BinBencher will be easier to install and run by the time the work is done some time in 2025.