# Lineagespot Lineagespot is a framework written in [R](https://www.r-project.org/), 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](https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format)). ## Installation ```r # install.packages("devtools") devtools::install_github("BiodataAnalysisGroup/lineagespot") ``` ## Raw data analysis The processing steps of the raw fastq files can be found [here](inst/scripts/raw-data-analysis.md). ## Citation If you use the tool, please cite the following work: Nikolaos Pechlivanis, Maria Tsagiopoulou, Maria Christina Maniou, Anastasis Togkousidis, Evangelia Mouchtaropoulou, Taxiarchis Chassalevris, Serafeim Chaintoutis, Chrysostomos Dovas, Maria Petala, Margaritis Kostoglou, Thodoris Karapantsios, Stamatia Laidou, Elisavet Vlachonikola, Anastasia Chatzidimitriou, Agis Papadopoulos, Nikolaos Papaioannou, Anagnostis Argiriou, Fotis Psomopoulos, "_Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece_", medRxiv 2021.03.17.21252673; doi: [https://doi.org/10.1101/2021.03.17.21252673](https://doi.org/10.1101/2021.03.17.21252673)