rMAP-docker

This Docker image provides a ready-to-use environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data & profiling AMR, Mobilome & Virulome. It includes all required tools & dependencies, enabling reproducible, scalable analysis of NGS data in research & public health settings, particularly for low-resource environments.

rMAP: Rapid Microbial Analysis Pipeline

rMAP is a fully automated pipeline for profiling the resistome & other genomic features of ESKAPEE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species & Escherichia coli) pathogens using whole-genome sequencing (WGS) paired-end reads.

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Features

• Quality control of raw sequencing reads
• Trimming of adapters & low-quality bases
• De novo assembly of genomes
• Genome annotation (Prokka)
• Detection of antimicrobial resistance genes (AMR)
• Variant calling & SNP analysis
• Phylogenetic tree construction (IQ-TREE)
• Pangenome analysis (Roary)
• Mobile Genetic Element (MGE) profiling
• SRA data download support

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Docker image🐳

The Docker image is hosted on DockerHub:

docker pull gmboowa/rmap:1.0

docker run -it --rm gmboowa/rmap:1.0

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Usage

Let’s say you have this '~/rmap_project' directory on your computer:

Basic docker run command

docker run -it --rm \

  -v ~/rmap_project:/data \
  
  gmboowa/rmap:1.0 \
  
  rmap --config /data/config.json
  
  

gmboowa/rmap:1.0: Your Docker image.

rmap --config /data/config.json: Runs rMAP using the configuration file inside the container.

Sample 'config.json' file

Here’s a minimal example of a config.json needed for rMAP (adjust paths & parameters as needed):

json

{
  "input_files": [
    "samples/sample1_R1.fastq.gz",
    "samples/sample1_R2.fastq.gz"
  ],
  "output_dir": "results/",
  "threads": 8,
  "reference_genome": "refs/bacteria_ref.fasta",
  "amr_database": "dbs/resfinder.fasta",
  "taxonomic_classification": true,
  "quality_control": true,
  "assembly": true,
  "variant_calling": true
}

**Note**:

Place the samples/, refs/, & dbs/ folders inside your local ~/data directory.

results/ will be created inside that directory too.

-v ~/data:/data: Mounts your local folder into the container.

Required options:

• -i/--input Path to input raw reads (.fastq or .fastq.gz)
• -o/--output Path to output directory
• -r/--reference Reference genome in .gbk format

Optional:

• -q/--trim Trimming quality threshold (default: 27)
• -a/--assembly Assembly tool: shovill or megahit
• -m/--amr Perform AMR profiling
• -vc/--varcall Perform variant calling
• -p/--phylogeny Perform phylogenetic tree construction
• -s/--pangenome Perform pangenome analysis

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Authors

• Gerald Mboowa
• Ivan Sserwadda
• Stephen Kanyerezi

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Resources

• GitHub: https://github.com/GunzIvan28/rMAP
• Issues: https://github.com/GunzIvan28/rMAP/issues

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License

This project is licensed under the MIT License. See the LICENSE file for details.