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We will now create a new CONDA environment to install the tools needed for mapping. The reason we need to create a new a new environments is because the QC and mapping tools have no compatible dependencies.

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Click on the link to the tool of interest and you will be presented with the conda command line to run in your system to install the tool:

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Copy and paste the first command shown line from above in into your terminal where you have activated the ‘ONTvariant’ conda environmentsessions with the activated ‘ONTvariants_mapping’ environment. Install samtools (version 1.20):

conda install bioconda::samtools

Next, let’s install minimap2 (version 2.28):

conda install bioconda::minimap2

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Alternative approach to create a conda env and install tools (we are not doing this - this just for your information) - installing all tools at once (slower option!)

Prepare the following environment.yml file:

name: ONTvariants_mapping
channels:
  - conda-forge
  - defaults
  - bioconda
dependencies:
  - samtools=1.20
  - minimap2=2.28

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As you have seen, we can search at anaconda.org for other tools that we might be interested to use.

Remember, if you run into compatibility issues or errors, you can always create a new conda environment for the tool of interest. NOTE: you can switch between conda environements as follows:

conda activate ONTvariants_QC
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conda deactivate
conda activate ONTvariants_mapping
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