- This repository contains the Nextflow script used to analyze wastewaster samples to idetify Antibiotic resistant genes.
- Nextflow
- Nextflow installation - https://www.nextflow.io/docs/latest/getstarted.html
- Requirement (Java version 17+)
- Docker or Conda
- Docker or conda used to run each process in Nextflow.
- Docker installation - https://docs.docker.com/engine/install/ubuntu/
- Conda download and installation - https://www.anaconda.com/
- Data files
- Human genome retrieved from NCBI. Human host contaminating reads removed from the wastewater samples.
- Ribosomal RNA reads from the SILVA database for multiple different species to leave behind messenger RNA for analysis.
We had a total of 24 samples for analysis collected across four sites. RNA was extracted from individual samples, libraries were prepared and sequencing caried out using a Miseq (Ilumina). We concatanated samples present in similar sites and ended up with four samples for analysis.