Run Binette

Binette will use the previously computed bins to refine and improve them, generating a new set of higher-quality bins.

To run Binette, use the following command:

#!/bin/bash
# Run Binette to refine and improve bins
binette --bin_dirs maxbin2_bins/ metabat2_bins/ semibin2_output/output_bins/ concoct_bins/ \
        -c Kickstart.megahit/R1.contigs.fa \
         -t 12 -o binette_output

⌛ Expected Time

This process should talke around 5 minutes to complete.

Once Binette completes, the binette_results directory should have the following structure:

binette_output/
├── final_bins
│   ├── binette_bin10.fa
│   ├── binette_bin11.fa
│   ├── binette_bin12.fa
│   ├── binette_bin13.fa
│   ├── binette_bin14.fa
│   ├── binette_bin15.fa
│   ├── binette_bin1.fa
│   ├── binette_bin2.fa
│   ├── binette_bin3.fa
│   ├── binette_bin4.fa
│   ├── binette_bin5.fa
│   ├── binette_bin6.fa
│   ├── binette_bin7.fa
│   ├── binette_bin8.fa
│   └── binette_bin9.fa
├── final_bins_quality_reports.tsv
├── input_bins_quality_reports
│   ├── input_bins_1.concoct_bins.tsv
│   ├── input_bins_2.maxbin2_bins.tsv
│   ├── input_bins_3.metabat2_bins.tsv
│   └── input_bins_4.semibin2_output_output_bins.tsv
└── temporary_files
    ├── assembly_proteins.faa.gz
    ├── diamond_result.log
    └── diamond_result.tsv.gz

Key Output Files:

• final_bins/: Contains the refined bins in FASTA format.

• final_bins_quality_reports.tsv: A summary report containing CheckM2 metrics for the final bin selection.

• input_bins_quality_reports/: Quality reports for each of the input bin sets from MaxBin2, MetaBAT2, CONCOCT, and SemiBin2.

Next Steps

In the next section, we will use final_bins_quality_reports.tsv along with the reports from binette_results/input_bins_quality_reports to visualize Binette’s bins and compare them with the initial bin sets.