gelidonyAMR: Salmonella Infantis Nextflow Pipeline

About GelidonyAMR

The name GelidonyAMR is inspired by the Gelidonya Lighthouse, a historic maritime landmark located on the southern coast of Türkiye, near Finike. Standing on a rugged cliff overlooking the vast Mediterranean, Gelidonya feels like the edge of the world—a place where time slows down, technology fades, and solitude takes over. It is one of the rare places where I can truly be alone, disconnected from everything yet deeply connected to nature.

Just as the lighthouse has guided sailors for centuries, GelidonyAMR serves as a bioinformatics beacon for detecting antimicrobial resistance (AMR) genes in Salmonella Infantis and other foodborne pathogens. Inspired by my personal connection to this remote and timeless place, this pipeline bridges ancient landscapes with cutting-edge technology, illuminating hidden threats in microbial genomes to safeguard public health.

Overview

This Nextflow pipeline, gelidonyAMR, has been developed for analyzing Salmonella Infantis genomes, including genome assembly, antimicrobial resistance (AMR) profiling, MLST and cgMLST typing. It is designed for use in a Conda environment and is part of the PhD project:

"Determination of Evolutionary Structure and Antimicrobial Resistance Profile of Salmonella Infantis"

Installation

Required Dependencies

Ensure that Conda is installed and up to date before proceeding. The following Conda packages must be installed to run the pipeline:

Create the Conda Environment

To create and activate the Conda environment for gelidonyAMR, use:

conda env create -f environment.yaml
conda activate gelidonyamr

If the environment is already created, simply activate it:

conda activate gelidonyamr

Additional Requirements

Abricate Databases

Ensure that the necessary AMR databases are installed:

abricate --setupdb
abricate --list

List all the required databases that have been used in this pipeline.

ChewBBACA Database

chewBBACA_downloadDB -sp "Salmonella" -o INNUENDO_salmonella

Reference Genome

The reference genome used in this pipeline:

• Organism: Salmonella Infantis
• Reference Accession: LN649235.1
• NCBI Assembly: GCA_000953495.1

Running the Pipeline

To execute the pipeline, use the following command:

nextflow run cinnetcrash/gelidonyamr --reads "../input_folder/*.fastq" --outdir Results -c config/nextflow.config

Environment Considerations

• This pipeline currently works only in a Conda environment.
• Docker support is planned for future releases.
• A similar pipeline is planned for Enterohemorrhagic Escherichia coli (EHEC).

Citation

The publication associated with this pipeline is not yet available. Updates will be provided when the citation is published.

Issues & Contact

If you encounter any issues while running the pipeline, please let me know.

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Pipeline developed by Gültekin Ünal