Course: Making sense of genomic data: COVID-19 web-based bioinformatics

Sequencing data can be saved in specific formats to make it easier to collect, store, analyse, and disseminate information. Each format will specify the manner in which each level of …

Introduction Amplicon sequencing is a highly targeted approach that enables researchers to analyse genetic variation in specific genomic regions. The ultra-deep sequencing of PCR products (amplicons) allows efficient variant identification …

During the lifecycle of SARS-CoV-2, varying genomic sequences contribute toward the creation of new virions. These virions (small, membrane-bound particles containing viral RNA) are formed within the infected host cell …

The genomic era was propelled forward by DNA sequencing techniques pioneered by numerous scientists in the 1970s. Fredrick Sanger developed the “chain-termination method”, now known as the “Sanger method”, in …

All of us have been impacted in some way by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). You are likely to be familiar with a city in China that you …

There are many sequencing technologies used for SARS-CoV-2 (Figure 1). In this step, we will approach a broadly used protocol based on viral whole-genome sequencing (WGS). The method consists of …

Pathogen genomics helps us to track the spread of an outbreak and to identify significant changes in the genome of a pathogen. This, in turn, helps us to identify the …

Introduction Identifying genomic variants can play an important role in scientific discovery as exemplified by the ongoing SARS-CoV-2 global surveillance. Variant calling involves identifying single nucleotide polymorphisms (SNPs), and small …

Did you ever ask someone what a new delicacy tastes like, and they respond with: “It tastes like chicken.” The truth is, that we use references all the time. It …

We would like to thank all those who were involved in the making of the course Making sense of genomic data: COVID-19 web-based bioinformatics Course Educators Carolina Castañeda Garcia PhD …

FastQC In order to analyse the quality of the raw data generated from next-generation high throughput sequencers, quality control (QC) reports need to be generated. FastQC is a popular tool …

Machines may be less error-prone than humans, but even machines can make mistakes. Or at the very least, they are only as good as the person/team who programmed them. The …

A useful range of COVID-19 and SARS-CoV-2 additional resources. Datasets for this course Zenodo repository: Making sense of genomic data: COVID-19 web-based bioinformatics Resources Coronavirus biology: ViralZone Coronavirus taxonomy: International …

Taking data and proceeding with analysis without first cleaning your data (also known as data wrangling) or without doing the necessary quality control can lead to inaccurate or even totally …

Presentations are an important part of the research process and allow the researcher a chance to illustrate the heart of their research to a public audience. The use of graphs …