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Let’s create an interactive session on the HPC:

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb

Install tools using conda

Approach #1 - installing tools one at a time (faster option)

Create a conda environment called sniffles

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Now we are done installing all the tools that we need for today.

Approach #2 (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
  - minimap=2-2.28

...

conda env create -f environment.yml

Installing more tools or dealing with compatibility issues between tools

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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Running mapping

Now that we have installed all the tools needed for the QC of Nanopore reads, let’s run the preprocessing of reads.

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Monitor the progress of the job:

qjobs

Visualisation of the alignment using IGV

We can visualise the mapped reads using a web-based IGV genome browser tool at https://igv.org

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