README.md
In nikopech/lineagespot: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Lineagespot
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).
Installation
# install.packages("devtools")
devtools::install_github("BiodataAnalysisGroup/lineagespot")
Raw data analysis
The processing steps of the raw fastq files can be found here.
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
nikopech/lineagespot documentation built on Dec. 28, 2021, 12:15 a.m.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Lineagespot
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).
Installation
# install.packages("devtools")
devtools::install_github("BiodataAnalysisGroup/lineagespot")
Raw data analysis
The processing steps of the raw fastq files can be found here.
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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