conda config --add envs_dirs /zfs/omics/projects/bioinformatics/software/miniconda3/envs/Binette
Introduction
Binette is a fast and accurate binning refinement tool designed to construct high-quality metagenome-assembled genomes (MAGs) from the output of multiple binning tools. It creates hybrid bins by applying set operations (intersection, difference, union) to overlapping bins and evaluates bin quality using CheckM2 (Mainguy and Hoede 2024).
Installation
Installed on Crunchomics: yes - the following versions of Binette are installed as part of the bioinformatics share:
- Binette v1.2.1
If you have access to Crunchomics and have not yet access to the bioinformatics share you can send an email with your UvA netID to Nina Dombrowski. Afterwards, you can add the bioinformatics share as follows (if you have already done this in the past, you don’t need to run this command):
If you want to install it yourself, the command below installs the version verified on Crunchomics. Before running it, check the tool’s GitHub for a newer version and swap the version number if one is available.
mamba create -n binette1.2.1 -c bioconda -c defaults -c conda-forge binette=1.2.1
# Add path to the checkm2 database (only run once)
conda activate binette1.2.1
checkm2 database --download --path add_your_desired_path/checkm/binette
export CHECKM2DB="add_your_desired_path/checkm/binette/uniref100.KO.1.dmnd"Usage
Input file format:
Binette accepts bin sets in one of two formats:
- Contig2bin tables [–contig2bin_tables]: Tab separated files of contig-IDs and bin-IDs, one table per binning tool (same format as used for DAS Tool, see DAS Tool):
Contig_1 bin.01
Contig_8 bin.01
Contig_42 bin.02
Contig_49 bin.03Bin directories [–bin_dirs]: One directory per binning tool, each containing the bins as separate fasta files.
Contigs [–contigs]: The full assembly in fasta format, containing all contigs referenced by the bin sets above.
Proteins (optional) [–proteins]: Predicted proteins in prodigal fasta format, to skip the gene prediction step.
Example for running Binette with contig2bin tables:
conda activate binette1.2.1
binette --contig2bin_tables bin_set1_contigs2bin.tsv bin_set2_contigs2bin.tsv \
--contigs assembly.fasta \
--outdir binette_output \
--threads 10Example for running Binette with bin directories (fasta files per bin):
binette --bin_dirs bin_set1_dir bin_set2_dir \
--contigs assembly.fasta \
--outdir binette_output \
--threads 10After running this, you will find the selected, non-redundant, high-quality bins along with a quality report in the specified output directory (binette_output above).
Options:
--version Show version and exit.
-h --help Show this message and exit.
Input Arguments:
-d --bin_dirs=<PATH> List of bin folders containing each bin in a fasta file.
-b --contig2bin_tables=<PATH> List of contig2bin tables with two columns: contig, bin.
-c --contigs=<PATH> Contigs in FASTA format. [required]
-p --proteins=<PATH> FASTA file of predicted proteins in Prodigal format (>contigID_geneID).
Skips the gene prediction step if provided.
Output and Runtime Control:
-o --outdir=<PATH> Output directory. [default: results]
--prefix=<TEXT> Prefix to add to final bin names (e.g. '--prefix sample1' will produce
'sample1_bin1.fa', 'sample1_bin2.fa'). [default: binette]
-t --threads=<INTEGER> Number of threads to use. [default: 1]
-v --verbose Enable verbose mode (show detailed debug information).
-q --quiet Enable quiet mode (only show warnings and errors).
--debug / --no-debug Activate debug mode. [default: no-debug]
--progress / --no-progress Show progress bar while fetching pangenomes (disable with
--no-progress). [default: progress]
--write-fasta-bins / --no-write-fasta-bins Write final selected bins as FASTA files (disable with
--no-write-fasta-bins). [default: write-fasta-bins]
Bin Filtering and Scoring:
--min_completeness=<INTEGER> Minimum completeness required for intermediate bin creation and
final bin selection. [default: 40]
--max_contamination=<INTEGER> Maximum contamination allowed for intermediate bin creation and
final bin selection. [default: 10]
--min_length=<INTEGER> Minimum length (bp) required for intermediate bin creation and
final bin selection. [default: 200000]
--max_length=<INTEGER> Maximum length (bp) allowed for intermediate bin creation and
final bin selection. [default: 10000000]
-w --contamination_weight=<FLOAT> Bins are scored as: completeness - weight * contamination. A lower
weight favors completeness over low contamination. [default: 2.0]
Advanced Options:
-e --fasta_extensions=<TEXT> FASTA file extensions to search for in bin directories (used with
--bin_dirs). [default: .fasta, .fa, .fna]
--checkm2_db=<PATH> Path to CheckM2 diamond database. By default the database set via
<checkm2 database> is used.
--low_mem Enable low-memory mode for Diamond.
--resume / --no-resume Resume mode: reuse existing temporary files if possible.
[default: no-resume]References
Mainguy, Jean, and Claire Hoede. 2024. “Binette: A Fast and Accurate Bin Refinement Tool to Construct High-Quality Metagenome Assembled Genomes.” Journal of Open Source Software 9 (102): 6782. https://doi.org/10.21105/joss.06782.