Installation
Prerequisites
Adapter Trimming: Trim Galore!
Deduplication: FastUniq
Alignment: VG Giraffe
Python3: Tested on 3.9, 3.10, 3.11 and 3.12. I would recommend 3.12 as it is the latest version and has the best performance.
VG: Tested from 1.49 to 1.63.1
1.61.0 is recommended at the moment: from 1.49 to 1.61 all seems fine, however the short read mapping speed is around 3 times slower than the previous versions.
Warning
You must ensure that both the VG toolkit and Python 3 are installed and added to your PATH.
Install via PIP
pip install methylGrapher
Install via CONDA
conda create -n methylGrapher python=3.12
conda activate methylGrapher
# Not recommended, but if you want to use conda to install vg, you can do so. Download VG from their release page instead.
conda install bioconda::vg
pip install methylGrapher