mtbmasker 0.1.0

Generate isolate-specific genome masks for Mycobacterium tuberculosis

mtbmasker

mtbmasker is a Python command-line tool designed to generate isolate-specific conservative genome masks for Mycobacterium tuberculosis (MTB) genomes. This is particularly useful for downstream variant calling and phylogenomic analyses by masking problematic genomic regions (e.g., PE/PPE genes, IS elements, and other repetitive loci).

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✨ Features

• Generates genome masks per isolate using BLASTn alignment against predefined repetitive genes.
• Supports custom isolate genome files and gene query sets.
• Automatically formats coordinates to BED, sorts, and merges overlapping masked regions.
• Outputs high-quality, isolate-specific .bed files for genome masking.

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🧬 Use case

This tool was originally developed for comparative genomics and transmission studies of Mycobacterium tuberculosis complex (MTBC) isolates, including M. africanum. It ensures that inter-lineage diversity is respected during masking.

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🔧 Installation

From GitHub (development version):

pip install git+https://github.com/EtienneNtumba/mtbmasker.git

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🚀 Usage

mtbmasker mask input_list.tsv --query-fasta data/genes_to_mask.fasta

Arguments:

• input_list.tsv — A tab-separated file with one isolate ID per line (without .fasta extension). Each ID must correspond to a ID.fasta file present in the working directory.
• --query-fasta — Fasta file of problematic/repetitive genes to be masked (default: data/genes_to_mask.fasta).

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📁 Example

input_list.tsv:

ARR1960.LR.Asm
QC-9.LR.Asm
N1177.LR.Asm

Each listed isolate must have a corresponding ARR1960.LR.Asm.fasta, etc., in the current directory.

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🔬 Requirements

• Python ≥ 3.8
• BLAST+
• BEDTools
• Typer

Both BLAST and BEDTools must be installed and available in your $PATH or via a conda environment.

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📄 Output

For each isolate, the following file is generated:

<isolate>_conservitive_AF19-like_masking_file.bed

This BED file contains sorted and merged coordinates of masked regions.

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📚 Citation

If you use this tool in your research, please cite:

Ntumba, E., Whiley, D., et al. (2025). [Manuscript Title], Journal Name, DOI: xxx

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📂 License

This tool is licensed under the MIT License.

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👥 Authors

• Etienne Ntumba Kabongo — Université de Montréal / McGill University
• Dan Whiley — Nottingham University