Kim Philipp Jablonski

TL;DR: It is shown how the popular workflow management system Snakemake can be used to guarantee reproducibility, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.

TL;DR: In this paper, the authors report a genomic analysis of SARS-CoV-2 in 48 raw wastewater samples collected from three wastewater treatment plants in Switzerland between July 9 and December 21, 2020.

TL;DR: In this paper , the authors used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.7 (Alpha), B.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level.

TL;DR: V-pipe as mentioned in this paper is a bioinformatics pipeline combining various state-of-the-art statistical models and computational tools for automated end-to-end analyses of raw sequencing reads.

TL;DR: This study estimates the transmission fitness advantage and the effective reproductive number of B.1.1-CoV-2 variant of Concern in Switzerland and quantifies the variant’s transmission Fitness advantage on a national and a regional scale.