Set Up the Tutorial Environment

To get started, we’ll download the necessary tools and set them up in a dedicated Conda environment.

Create a Conda Environment

First, let’s create a new Conda environment specifically for this tutorial:

conda env create -f binette_tutorial_env.yaml -n binette_tutorial

This command will create a Conda environment named binette_tuto using the environment file binette_tutorial_env.yaml.

Below is the content of the binette_tutorial_env.yaml file:

name: binette_tutorial
channels:
  - conda-forge
  - bioconda
dependencies:
  - sra-tools              # To get the tutorial initial data
  - fastqc                 # Quality control for high-throughput sequencing data
  - samtools=1             # Tools for manipulating sequencing data in SAM format
  - bedtools=2             # Suite of tools for genome arithmetic
  - bwa-mem2=2             # Align reads to a reference genome (using BWA-MEM2)
  - megahit=1              # De novo assembler for large genomes
  - maxbin2=2              # Binning tool for metagenomic datasets
  - metabat2=2             # Binning tool for metagenomic datasets
  - semibin=2              # Binning tool for metagenomic datasets
  - concoct=1              # Binning tool for metagenomic datasets
  - binette                # Binette for binning and genome analysis
  - das_tool=1             # Bin refiner to compare with Binette
  - jupyter                # Jupyter notebook for interactive analysis
  - pandas                 # Data manipulation and analysis
  - plotly=5               # Interactive graphing

Please ensure that the Checkm2 database is installed as described in the installation documentation. You can find the instructions here.

Activate the Environment

After the environment is created, activate it by running:

conda activate binette_tutorial