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: Wiki

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 . 

Once I have a stable version release, I will upload them to conda and pip as well

Running the code

Note: This code works only on paired end metagenomes for now.

This workflow is made modular;

1. mitobee run If there is a representative closely related genome mitogenome, provide that as the host seq and get started

    #Running mitobee with test files available in the repo
    mitobee run --input test-files/metagenomes --extn fastq.gz \
         --pattern_r1 _R1 --pattern_r2 _R2 \
         --host_seq test-files/am-dh4.fasta \
         --output output

2. mitobee tree Once the mitochondrial genomes are built from each metagenome sample, run this module to build a tree with these mitogenomes and other references

    #After the mitogenomes are made from the mitobee run results. Add other references to build a tree
    #Once again example with test files
    mitobee tree --input test-files/mitogenomes --extn fasta --output output -k all

3. mitobee search If there is a no closely related mitogenome available, then this step can be run first to search against a set of mitogenomes or mito genes This module will provide an overview of which reference to use

    #If a closely related mitochondrial genome is not available, but a gene is, like cox  or rRNA genes
    #Download the reference genes you would like to use of the closely related genomes

    #to search against mitogenomes refernece set
    mitobee search --input test-files/mitogenomes --extn fastq.gz \
        --pattern_r1 _R1 --pattern_r2 _R2 \
        --ref_seq  test-files/ref-set-genome --output output \
        -k all --mode mitogenome

    #to search against mitogenomes refernece gene set 
    mitobee search --input test-files/mitogenomes --extn fastq.gz \
        --pattern_r1 _R1 --pattern_r2 _R2 \
        --ref_seq  test-files/ref-set-genes --output output \
        -k all --mode genes 

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