It is also possible to create a “bioinformatic environment” within Bioconda, where all
software tools used for your analysis are “stored,” but you do not have to! For more details
read: https://uoa-eresearch.github.io/eresearch-cookbook/recipe/2014/11/20/conda/.
Due to the fact that we are using our computer only for bioinformatic purposes, we just
add all software tools into the bin folder of miniconda3 and add the path to our .bashrc.
Some other helpful commands:
A list of all available Bioconda software tools can be found at https://bioconda.github.
io/conda-recipe_index.html.
If you want to install some new tools via run
in the terminal.
The following table (Table 5.1) contains the most important and helpful tools to perform
NGS data analysis.
The most time saving and easiest way to download the bioinformatic packages via
Conda is to create a .txt file with all the package names.
Another important tool for Variant discovery based on NGS data is the Genome
Analysis Toolkit. The latest download release can be found here (https://github.com/
broadinstitute/gatk/releases/download/4.1.8.0/gatk-4.1.8.0.zip).
5 Computer Setup
63