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This is the development version of lineagespot; for the stable release version, see lineagespot.

Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

Bioconductor version: Development (3.20)

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). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.

Author: Nikolaos Pechlivanis [aut, cre] , Maria Tsagiopoulou [aut], Maria Christina Maniou [aut], Anastasis Togkousidis [aut], Evangelia Mouchtaropoulou [aut], Taxiarchis Chassalevris [aut], Serafeim Chaintoutis [aut], Chrysostomos Dovas [aut], Maria Petala [aut], Margaritis Kostoglou [aut], Thodoris Karapantsios [aut], Stamatia Laidou [aut], Elisavet Vlachonikola [aut], Aspasia Orfanou [aut], Styliani-Christina Fragkouli [aut], Sofoklis Keisaris [aut], Anastasia Chatzidimitriou [aut], Agis Papadopoulos [aut], Nikolaos Papaioannou [aut], Anagnostis Argiriou [aut], Fotis E. Psomopoulos [aut]

Maintainer: Nikolaos Pechlivanis <inab.bioinformatics at>

Citation (from within R, enter citation("lineagespot")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

lineagespot User Guide HTML R Script
Reference Manual PDF


biocViews Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Imports VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils
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Suggests BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0)
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Source Package lineagespot_1.9.0.tar.gz
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macOS Binary (x86_64) lineagespot_1.9.0.tgz
macOS Binary (arm64) lineagespot_1.9.0.tgz
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