Registration Open for Bioc2024
Early registration discount pricing ends May 31!


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

Bioconductor version: Release (3.19)

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))


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 1.8.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Imports VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils
System Requirements
Bug Reports
See More
Suggests BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0)
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package lineagespot_1.8.0.tar.gz
Windows Binary
macOS Binary (x86_64) lineagespot_1.8.0.tgz
macOS Binary (arm64) lineagespot_1.8.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats