pangolin

This is a SARS-CoV-2 sequencing project done at the BSSE relying on V-pipe (doi:10.1093/bioinformatics/btab015) to analyse Illumina data done on positive swabs test samples for the genomic surveillance of the COVID-19 pandemic in Switzerland and on wastewater samples provided by EPFL and Eawag.

pipeline

for the V-pipe pipeline, see:

• tutorial: https://cbg-ethz.github.io/V-pipe/tutorial/sars-cov2/ (video tutorial)
• SARS-CoV-2 subpage: https://cbg-ethz.github.io/V-pipe/sars-cov-2/
• main website: https://cbg-ethz.github.io/V-pipe/
• github repo: https://github.com/cbg-ethz/V-pipe

wastewater

for the code used in wastewater analysis, see:

• https://github.com/cbg-ethz/cojac

video presentation

Short Oral presentation done at the ECCVID conference in September 2020:

• https://youtu.be/BJ-un88CT9A