Background

This project is a successor to the C-WAP pipeline and is intended to process SARS-CoV-2 wastewater samples to determine relative variant abundance.

⚠️Warning⚠️

The results generated by this pipeline are not CLIA certified and should not be considered diagnostic.

Introduction¶

CDCgov/aquascope is a bioinformatics best-practice pipeline for early detection of SARS-COV variants of concern, sequenced throughshotgun metagenomic sequencing, from wastewater.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible.

Pipeline summary¶

1. Read QC: FastQC
2. Trimming reads: Fastp
3. Aligning short reads: Minimap2
4. Freyja Variant classification: Freyja
5. Present QC for raw reads: MultiQC