Course: A Practical Guide for SARS-CoV-2 Whole Genome Sequencing

COG-UK and similar sequencing-based surveillance responses to the pandemic around the world resulted in millions of genome sequences becoming available. As well as the possibility of understanding the evolution of …

Pangolin (Phylogenetic Assignment of Named Global Outbreak Lineages) is a piece of software created by the same team that proposed the Pango nomenclature scheme, which we discussed earlier in the …

Nextclade is a free and open-source tool for viral genome alignment, mutation calling, clade assignment, quality checks, and phylogenetic positioning. It can rapidly assess viral genomes by running a series …

A growing number of biological topics may now be understood, thanks to high-throughput sequencing methods. These technologies have continued to advance, and, most recently, long-read sequencing has expanded its applications …

Reference alignment and consensus sequence generation There are many analyses that can be done with a sample’s FASTQ reads, but here we will focus on reference alignment. This is typically …

Demultiplexing As sequencers create large numbers of reads, the library being sequenced can consist of multiple samples that are pooled together for sequencing. To determine which reads have come from …

Sequencing platforms There are several different sequencing platforms commercially available. Although we focus here on those developed by Illumina and Oxford Nanopore Technologies (ONT), other available platforms include PacBio by …

Illumina Sequencing run metrics Run performance for Illumina sequencing can be monitored using the Illumina native programmes: Sequencing Analysis Viewer (SAV) and BaseSpace. Next, we will discuss the key metrics. …

Library preparation is the first step of next-generation sequencing (NGS), preparing your samples to allow them to bind to the flow cell and be identified. This article will briefly guide …

Next-generation sequencing has revolutionised genomic research, allowing high-throughput profiling of genomes, transcriptomes, DNA-protein interactions and more. This is achieved by performing millions to billions of massively parallel short read (50-500bp) …

Genome sequencing of SARS-CoV-2 involves performing PCR using ARTIC or Midnight protocol. PCR amplification is the common step involved in both protocols. In order to confirm the successful PCR amplification, …

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) hold the genetic information required to make proteins, and therefore all life on earth. The sequence in which DNA bases occur provides the …

Different targeted methods have been developed to library preparation and sequence full-length SARS-CoV-2 genomes from specimens containing both viral and human nucleic acids. Due to the size difference between the …

The extraction of RNA from viral samples is an important step for pathogen research. Viral nucleic acid extraction is the first step for downstream genomic analysis. Analysis of viruses in …

To ensure that work is performed accurately and consistently, it is important to put quality management systems in place (Figure 1). This limits error and expedites troubleshooting, thus saving resources …