MEGAHIT (WSL)

MEGAHIT is a fast and memory-efficient assembler for metagenomic sequencing data. There are several ways to install MEGAHIT, but the easiest way is using conda.

On WSL systems, conda is often not installed by default, so you will need to install it first.

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1. Install conda

1. Go to https://repo.anaconda.com/archive/ and download the appropriate installer for your system. - For example, for WSL: Anaconda3-2024.06-1-Linux-x86_64.sh

2. Open your terminal and download using wget:

   wget https://repo.anaconda.com/archive/Anaconda3-2024.06-1-Linux-x86_64.sh
   

3. Run the installation script:

   bash Anaconda3-2024.06-1-Linux-x86_64.sh
   

4. Read the license agreement and follow the prompts to accept.

5. Close WSL and open it again.

6. Test that conda is installed:

   conda
   

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2. Install MEGAHIT using conda

conda install -c bioconda megahit

• If prompted, select y to proceed.

• Test the installation:

megahit --help

• If this does not work, follow alternative installation methods: https://github.com/voutcn/megahit

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MEGAHIT (Mac)

1. Install Miniconda

• Download the installer (pkg recommended) from:

  https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.pkg

• Check installation:

conda --version

• If prompted, select y to proceed.

2. Install MEGAHIT using conda

conda install bioconda::megahit