Software

lineagespot

Lineagespot is a Bioconductor package 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.

Material

• github

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

tripr

is a Bioconductor package, written in shiny that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. Every step of the analysis can be performed interactively, thus not requiring any programming skills. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.

Functions for an R command-line use are also available.

Installation

tripr is distributed as a Bioconductor package and requires R (version “4.1”), which can be installed on any operating system from CRAN, and Bioconductor (version “3.14”).

To install tripr package enter the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("tripr", version="devel")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

Launching the app

Once tripr is successfully installed, it can be loaded as follow:

library(tripr)

Material

• github