# Research Object Crate for ARG-Sniper: A Nextflow pipeline for antibiotic resistance gene detection from paired-end sequencing reads.

Original URL: https://workflowhub.eu/workflows/2080/ro_crate?version=1

# ARG-Sniper A Nextflow pipeline for antibiotic resistance gene detection from paired-end sequencing reads. ## Introduction ARG-Sniper is a Nextflow DSL-2 pipeline designed for metagenomic analysis that processes paired-end FASTQ files to detect antibiotic resistance genes using multiple bioinformatics tools. The pipeline runs five different analysis tools in parallel: GROOT, ARIBA, KMA (adopted from ARGprofiler), KARGA, and SRST2, each requiring their respective databases. Users can selectively skip any of the five tools using command-line flags (--skip_groot, --skip_ariba, etc.), allowing for customized analysis workflows. The pipeline takes FASTQ and processes them through the selected tools. After individual tool execution, the pipeline collects all results and generates a summary report that consolidates findings from each analysis. The workflow outputs separate directories for each tool's results along with a final summary directory containing the integrated analysis. Note: This pipeline focuses on detecting antibiotic resistance genes and does not report SNP-based resistance mechanisms. ## How-2-Run Before running the pipeline make sure all the required databases and tool-dependencies were met. ### Software Requirements - **Nextflow** (≥22.04.0) with DSL-2 support - **Singularity** container runtime ### Bioinformatics Tools (via Singularity containers) - **SRST2** v2.0.0 - Short Read Sequence Typing - **GROOT** v1.1.2 - Graph-based resistance gene detection - **ARIBA** v2.14.6 - Antimicrobial Resistance Identification - **KARGA** v1.02 - K-mer based resistance gene analysis - **KMA** v1.4.9 - K-mer alignment tool (used by ARGprofiler) ### Required Databases All tools require pre-built databases from the panARG v2 collection: - grootdb (indexed database) - aribadb (prepared database) - srst2db (FASTA sequences) - kargadb (FASTA sequences) - argprofilerdb (KMA indexed database) - panARG annotations (TSV metadata file) ### System Requirements - **CPU:** 8 cores (default) - **Memory:** 16 GB RAM (default) - **Scheduler:** SLURM (for HPC execution) ### Usage Run `--help` to see available options: ```bash nextflow run ARG-sniper/main.nf --help ``` ``` Usage: nextflow run ARG-Sniper-pipeline.nf --offline -with-report Required Arguments: Input: --reads Folder containing reads with file name *_R{1,2}.fastq.gz --gootdb Path of indexed GROOT database --aribadb Path to ARIBA database --kargadb Path to KARG database --srst2db Path to SRST2 database --argprofilerdb Path to ARGprofiler database --output Folder for output files # By default, the pipeline will run all supported tools. Optional Arguments: Skipping specific tools: --skip_groot Skip running GROOT --skip_kma Skip running KMA --skip_ariba Skip running ARIBA --skip_karga Skip running KARGA --skip_srst2 Skip running SRST2 ``` ## Expected Output Upon successful execution with all tools, ARG-Sniper generates the following directory structure with results for each sample: ``` results/ ├── argprofiler_results/ │ └── ARGprofiler_report_{sample}.txt ├── ariba_results/ │ ├── ariba_report_{sample}.tsv │ └── ariba_summary_{sample}.csv ├── groot_results/ │ └── groot_report_{sample}.tsv ├── karga_results/ │ └── karga_report_{sample}.csv ├── srst2_results/ │ └── srst2_report_{sample}_fullgenes_sequence_results.txt └── summary/ └── summary_{sample}.tsv ``` **Example output for multiple samples:** ``` results/ ├── argprofiler_results/ │ ├── ARGprofiler_report_dataset-100x-depth.txt │ ├── ARGprofiler_report_dataset-90x-depth.txt │ └── ARGprofiler_report_dataset-95x-depth.txt ├── ariba_results/ │ ├── ariba_report_dataset-100x-depth.tsv │ ├── ariba_report_dataset-90x-depth.tsv │ ├── ariba_report_dataset-95x-depth.tsv │ ├── ariba_summary_dataset-100x-depth.csv │ ├── ariba_summary_dataset-90x-depth.csv │ └── ariba_summary_dataset-95x-depth.csv ├── groot_results/ │ ├── groot_report_dataset-100x-depth.tsv │ ├── groot_report_dataset-90x-depth.tsv │ └── groot_report_dataset-95x-depth.tsv ├── karga_results/ │ ├── karga_report_dataset-100x-depth.csv │ ├── karga_report_dataset-90x-depth.csv │ └── karga_report_dataset-95x-depth.csv ├── srst2_results/ │ ├── srst2_report_dataset-100x-depth_fullgenes_sequence_results.txt │ ├── srst2_report_dataset-90x-depth_fullgenes_sequence_results.txt │ └── srst2_report_dataset-95x-depth_fullgenes_sequence_results.txt └── summary/ ├── summary_dataset-100x-depth.tsv ├── summary_dataset-90x-depth.tsv └── summary_dataset-95x-depth.tsv ``` The `summary/` directory contains consolidated results from all tools for each sample.

Author
  Sumeet Tiwari, Sam Haynes
License
  Apache-2.0

## Contents

Main Workflow: ARG-Sniper: A Nextflow pipeline for antibiotic resistance gene detection from paired-end sequencing reads.
Size: 4944 bytes