Installation

Recommended Environment

The project ships with a micromamba/conda environment definition at envs/srna-imp.yaml.

micromamba create -p /scratch/users/pmay/sRNA/sRNA-IMP/.micromamba/envs/srna-imp -f envs/srna-imp.yaml
micromamba activate /scratch/users/pmay/sRNA/sRNA-IMP/.micromamba/envs/srna-imp

Core Runtime Tools

Important tools include: - fastp - fastqc - bowtie and bowtie-build - samtools - bedtools - bwa - srnaMapper - kraken2 - ribodetector_cpu - cmscan - RNAfold - multiqc

Source Code

The main entrypoint is scripts/srna_imp.py.