Using Bioconda

Bioconda is a distribution of bioinformatics software accessible through the Conda package manager. Your Conda environment must first be configured to set up Bioconda before you can access the packages available through it. To do this, first you must set up and open a conda virtual environment through miniforge, instructions for doing so are located here.

Once that is done, you can set up bioconda by typing the following commands

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

After that, you can install bioconda packages like anaconda packages. For example, to install the samtools package:

conda install bioconda::samtools

Popular Bioconda Packages

• samtools - for interacting with and post-processing high throughput sequencing data in SAM, BAM, anc CRAM formats
• htslib - C library for high throughput sequencing data
• pysam - python package for high throughut sequencing
• bedtools - genomics analysis
• blast - sequence alignment