MitoBee

Snakemake workflow to get mitogenomes from metagenomic data

Still under development! Stable release out as a version, but only if there is a closely related mitogenome available.

Documentation: Read the Docs

Install

Source install Run the below commands:

git clone https://github.com/npbhavya/MitoBee.git
cd MitBee
mamba create -y -n mitobee python=3.13
conda activate mitobee
pip install -e . 

Input files

Input files:

• Input directory with metagenomes
• Reference directory
  • If running run or tree module, provide a (one) reference genome.
  • If running gene module, provide a reference gene set

Output files

Output files: Provide the output folder, contains subdirectories

• PROCESSING: Folder containing intermediate files
• REPORTS: Final results including the mitogenome fasta files from (hopefully) each metagenome sample
  Also inlcudes the QC reports, to include stats on how many reads were processed, and not