Phorager

Prophage Analysis Pipeline

A comprehensive pipeline for bacterial genome quality control, prophage detection, and prophage characterization

Authors:

• Xena Dyball
• James Docherty
• Alise Ponsero
• Ryan Cook

Citation: [Paper Citation or Preprint Link]

Overview

Phorager provides an integrated workflow for:

• Bacterial genome quality control - CheckM2 assessment, filtering, and dRep dereplication
• Prophage detection - GenoMAD and ...

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 ...