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How to detect an outbreak

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 …

Lineages classification using Pangolin

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 …

Interpreting Nextclade quality metrics

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 …

Why high-quality data is important

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 …

User-friendly tools for quality control

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 …

How to generate a consensus sequence

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 …

Accessing and using sequencing data

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 …

What are sequencing metrics

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. …

Comparing library preparation methods

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 …

What is a sequencing library and how is it prepared?

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) …

Checking the quality of amplicons

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, …

Producing SARS-CoV-2 amplicons

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 …

What a targeted sequencing protocol

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 …

How to isolate good quality nucleic acids

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 …

How to implement quality management

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 …