Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format).
# install.packages("devtools")
devtools::install_github("BiodataAnalysisGroup/lineagespot")The processing steps of the raw fastq files can be found here.
If you use the tool, please cite the following work:
Pechlivanis, N., Tsagiopoulou, M., Maniou, M.C. et al. Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece. Sci Rep 12, 2659 (2022). https://doi.org/10.1038/s41598-022-06625-6