Getting started

Prerequisites

To run the workflow you need to have mamba (conda also works) and snakemake installed.

All other software required by NanoITs will be installed by snakemake for you in a conda environment.

Information about installing mamba can be found here and for conda can be found here.

After having installed conda/mamba you can install snakemake as follows. Notice, the workflow was so far tested with snakemake version 7.32.4.

mamba create --name snakemake -c conda-forge -c bioconda snakemake=7.32.4 python=3.11.6

NanoITS can be installed via git:

git clone https://github.com/ndombrowski/NanoITS.git

If you do not have git installed, you can also download the folder from github. Therefore: