In nikopech/lineagespot: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

## For links
library("BiocStyle")
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knitr::opts_chunk$set(
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Introduction

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.

Quick start

Installation

lineagespot 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 lineagespot package enter the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("lineagespot")
## Check that you have a valid Bioconductor installation
BiocManager::valid()

Raw data analysis

Example fastq files are provided through zenodo. For the pre processing steps of them, the bioinformatics analysis pipeline is provided here.

Running lineagespot

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

library(lineagespot)

lineagespot can be run by calling one function that implements the overall pipeline:

results = lineagespot(vcf_folder = system.file("extdata", "vcf-files", 
                                                package = "lineagespot"),

                      gff3_path = system.file("extdata", 
                                              "NC_045512.2_annot.gff3", 
                                              package = "lineagespot"),

                      voc = c("B.1.1.7", "B.1.617.2", "B.1.351"))

Explore the results

The function returns three tables:

• An overall variant table containing all variants included in the input VCF files, along with the related information (gene, location etc.)

# overall table
head(results$variants.table)

• A table with the identified overlaps/hits between the variant table and the given lineage reports.

# lineages' hits
head(results$lineage.hits)

• A lineage report table where metrics for the abundance of each lineage are computed. To this end, the mean AF (allele frequence) of the variants per lineage, the mean AF of the unique variants per lineage and the non-zero min. AF of the lineage's unique variants are computed. Moreover given a AF threshold the number of variants in each sample is computed along with the resulting proportion (Number of variants to the number of lineage rules).

# lineagespot report
head(results$lineage.report)

Session info {.unnumbered}

Here is the output of sessionInfo() on the system on which this document was compiled running pandoc r rmarkdown::pandoc_version():

sessionInfo()

nikopech/lineagespot documentation built on Dec. 28, 2021, 12:15 a.m.