Code to replicate the early detection analysis of SARS-CoV-2 variants from deep sequencing samples

In this repository we provide the code to replicate the early detection analysis of SARS-CoV-2 variants from deep sequencing samples.

We provide in the directory named "1_variant_calling" the adopted variant calling pipeline for SARS-CoV-2 paired-end Illumina amplicon sequencing data. Moreover, we provide in the directory named "2_mutations_annotation", an R script to perform amino acid annotation for nonsynonymous mutations.

Please feel free to contact us if you have any question on the pipeline at: [email protected]