ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants.

Valentin TilloyPierre CuzinLaura LeroiEmilie GuérinPatrick DurandSophie Alain

Published in: PloS one (2022)

ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers. Pipeline is implemented and available at https://gitlab.com/vtilloy/aspicov.

Keyphrases

sars cov
data analysis
respiratory syndrome coronavirus
signaling pathway
copy number
oxidative stress
lps induced
clinical practice
nuclear factor
pi k akt
loop mediated isothermal amplification
cell proliferation
toll like receptor
dna methylation
quantum dots
high throughput sequencing