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Expand Up @@ -16,16 +16,6 @@ The current software includes:
- [LolliPop](https://github.com/cbg-ethz/LolliPop): Integrated into V-pipe, component tool for kernel-based deconvolution of variants



# CAVEAT: Pre-release

We're currently in the process of integrating most of the processing into V-pipe.
A prototype of this integration is available in branch [ninjaturtles](https://github.com/cbg-ethz/V-pipe/tree/ninjaturtles), and the latest version is now config file-based and can be adapted to other sites.

There is no tutorial, yet. In the mean time, a [draft _HOWTO_](https://gist.github.com/DrYak/e28d5d523e644ea455748d540a32ad4d) can help you understand the details and deploy V-pipe in your own setting.



# Introduction

This readme file describes the procedure that is used since 2023-04-08 to prepare the wastewater-based SARS-CoV-2 prevalence display on [CoV-Spectrum](https://cov-spectrum.ethz.ch/story/wastewater-in-switzerland) and provide the data to [BAG/FOPH](https://www.covid19.admin.ch/en/epidemiologic/waste-water). The main references are [doi:10.1038/s41564-022-01185-x](https://doi.org/10.1038/s41564-022-01185-x) (preprint: [doi:10.1101/2021.01.08.21249379](https://www.medrxiv.org/content/10.1101/2021.01.08.21249379)), and [doi:10.1101/2022.11.02.22281825](https://doi.org/10.1101/2022.11.02.22281825).
Expand All @@ -39,13 +29,11 @@ It relies on V-pipe for most of the processing. The key steps are:
A separate procedure documents the steps to [add a new variant](#add-a-new-variant).



# Add a New Variant

**TODO** (TO BE DOCUMENTED, [check HOWTO for now](https://gist.github.com/DrYak/e28d5d523e644ea455748d540a32ad4d#signatures-for-variants))



# Base processing

Sample data is processed using the same pipeline configuration as was used to process NGS data for the [Swiss SARS-CoV-2 Sequencing Consortium (S3C)](https://bsse.ethz.ch/cevo/research/sars-cov-2/swiss-sars-cov-2-sequencing-consortium.html).
Expand Down Expand Up @@ -148,11 +136,6 @@ In the directory `pangolin/working`, submit the job `vpipe-noshorah.bsub` (LSF)
This will run the initial steps of V-pipe but stop before calling SNV and local haplotypes with ShoRAH.



# Coocurrence analysis

> **Note** COJAC _**is now**_ part of V-pipe.

## Installation

Processing uses the V-pipe.
Expand Down Expand Up @@ -253,7 +236,6 @@ Manually edit and adapt `work-vp-test/var_dates.yaml` (the list of all variant w
# Wastewater analysis

> **Note**
> - LolliPop _**is now**_ part of V-pipe and runs the deconvolution
> - unlike the notebook `cojac/notebooks/ww_smoothing.ipynb` used in the [Nature Microbiology article](https://doi.org/10.1038/s41564-022-01185-x), posterior probabilities of the local haplotype generated by ShoRAH are not taken into account, and the curves are built using LolliPop's kernel based deconvolution which is both more robust against variants that share mutations in their exhaustive lists, and able to leverage the time component to compensate the extreme over-dispersion of typical wastewater samples. See [LolliPop's preprint](https://doi.org/10.1101/2022.11.02.22281825) for details.

## Installation
Expand Down