Omicron variants

In this post, I describe a simple workflow for identifying Omicron variants from some sequencing data shared by the Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP) and the Centre for Epidemic Response and Innovation (CERI). To follow the workflow, you need to have Docker installed and an Internet connection. To get started, run a container…

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Sequence analysis of SARS-CoV-2 part 3

This post is a continuation of a series of posts on the sequence analysis of SARS-CoV-2; see part 1 and part 2 if you haven’t already. Since my first post, I found out that you can blast sequences against a Betacoronavirus database on NCBI BLAST. The database, as of 2020/03/10, has a total of 7,844…

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Sequence analysis of SARS-CoV-2 part 2

I ended my previous post on the sequence analysis of SARS-CoV-2 with the amino acid alignment of the spike protein from SARS-CoV-2 (MN908947) and Bat coronavirus RaTG13 (MN996532). The spike protein is of specific interest as it is due to its binding with the angiotensin converting enzyme 2 (ACE2) receptor that it is able to…

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Sequence analysis of SARS-CoV-2

The article “A new coronavirus associated with human respiratory disease in China” released the full genome sequence (29,903 nt) of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the paper, meta-transcriptomic sequencing was performed on bronchoalveolar lavage fluid (BALF) from a 41 year old male suffering from a severe respiratory disease. Contigs were assembled using…

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