NGS-SA: Genomic and Bioinformatic protocols to SARS-CoV-2

SARS-COV-2 genome assembly using Genome Detective

Title: SARS-COV-2 genome assembly using Genome Detective

Authors: Koen Deforche, Houriiyah Tegally and Tulio De Oliveira

Date: 2020-06-20


This protocol describes the procedure for generating SARS-CoV-2 genomes in fasta file. It accepts as input files fastq files from Illumina, Oxford Nanopore Technologies (ONT) and Ion Torrent sequencers. The protocol has three steps. The first step involves the analysis of fastq files by Genome Detective. The second step involves mutation filtering using genotype likelihood calculations with a bash script that access bcftools and mpileup (Download: Illumina scripts and ONT scripts). The third step involves visual validation of mutations using a bam file viewer, such as Geneious.


Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes. Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T. Bioinformatics, 2020. DOI:

Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data.Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T, Bioinformatics (2019), DOI: 10.1093/bioinformatics/bty695.


A) Access Protocol at website (Recommended format)

B) Access Protocol in PDF format (Specific laboratory format)