🧬 PointMap

A lightweight pipeline for extracting genes and mapping point mutations across bacterial genomes.

PointMap extracts a target gene from multiple genomes, translates the sequences, aligns all proteins, and identifies amino-acid point mutations relative to a user-provided reference gene. It works with any bacterial species and any target gene.

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🚀 Features

• Locate the target gene in both the reference genome and all sample genomes
  (Prokka annotation + bedtools extraction + BLAST search)
• Extract nucleotide sequences and generate amino-acid sequences for all genomes
  (Prokka-based translation)
• Align all protein sequences to the reference using MAFFT
• Detect amino-acid point mutations relative to the reference sequence

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📦 Installation

Clone the repository:

git clone https://github.com/sbenvari/PointMap.git
cd PointMap

Create the environment:

conda create -n pointmap
conda activate pointmap
conda env update -f environment.yml

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📁 Required Inputs

1. Reference sample

Supported formats: .fasta, .fa, .fna

Example (included in repo):

example_ref/
 └── haemo_reference.fna

2. Directory of genome assemblies

Supported formats: .fasta, .fa, .fna

Example (included in repo):

example_genome/
 └── GCA_000009865.fna

3. Gene name

Used for naming outputs (e.g., gyrA, parC, rpoB).

4. Output directory name

A folder that PointMap will create.

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▶️ Usage

General syntax:

./pointmap.sh <REFERENCE_GENOME> <GENOMES_DIR> <GENE_NAME> <OUTPUT_DIR>

Example — Extract and map mutations in gyrA:

./pointmap.sh path/to/haemo_reference.fna path/to/genomes/ gyrB test_output

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📂 Output Structure

output_dir/
 ├── sequences_ref/         # Extracted reference gene sequence
 ├── sequences_samples/     # Extracted sample gene sequences
 ├── prokka_out/            # Prokka annotations
 ├── protein/               # Translated protein FASTAs
 ├── multi_sequences.faa    # All proteins concatenated
 ├── aligned_sequences.faa  # MAFFT alignment
 └── mutations_<gene>.txt   # Final mutation list

Example mutation output:

isolate1   S84L,E88K
isolate2   No mutations
isolate3   S84A

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📧 Contact

For issues, bugs, or feature requests, please open an issue on GitHub.