A workflow for quantifying SARS-CoV-2 lineage abundances (e.g., B.1.167.2 aka Delta) in short-read paired-end sequencing data of wastewater.
This workflow is written in Snakemake. Its installation instructions and usage are described in the Snakemake Workflow Catalog.
After you run the workflow, you can find its main output under results/. The .zip file contains a detailed self-contained HTML report encompassing runtime statistics, provenance information, workflow topology, and results. This report can be passed on to collaborators, provided as a supplementary file in publications, or uploaded to a service like Zenodo in order to obtain a citable DOI.
A realistic example report from this workflow can be found here.
The results are split into two sections. First, the abundance estimations of SARS-CoV-2 are displayed.
The horizontal axis shows the lineage abundances in the sample; the vertical axis shows the called lineage. Lineages below 0.02 are summarized under the term "other".
The estimation is performed with Kallisto, taking the SARS CoV-2 Wuhan Sequence NC_045512.2 as a predefined reference.
The second section display several metrics related to the sequencing itself.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or the following:
@misc{sars-cov-2-wbe,
author = {Thomas Battenfeld},
title = {SARS-CoV-2 Wastewater Based Ecology},
year = {2021},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/thomasbtf/sars-cov-2-wbe}}
}