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.
The results generated by this pipeline are not CLIA certified and should be used for research purposes only.
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 easy and results highly reproducible.
Please visit our user-guides.
Aquascope was developed in collaboration by OAMD's SciComp Team, the National Wastewater Surveillance System (NWSS), and the DCIPHER Team at Palantir.
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.