![]() ARTIC original used the ONT ligation sequencing kit and therefore all reads produced are equivalent to the amplicon length. In addition to the amplicon length the key difference between the Midnight protocol and the original ARTIC protocol with Nanopore sequencing is the library preparation method. These primers were designed using primalscheme by Quick et. The amended Midnight protocol uses longer 1200bp amplicons first proposed in a publication by Freed et. This enables full genome coverage even in situations where viral RNA might be more degraded or is present at low number of copies. This protocol relies on 98 overlapping ~400bp amplicons split into two pools. There are many methods to sequence the genome of SARS-CoV-2 but one of the most popular remains the ARTIC Network protocol. First the rapid publication of the original sequence from Wuhan to ongoing surveillance to identify and track the emergence of variants of the virus that could be a public health concern. Sequencing of SARS-CoV-2 has been pivotal in the ongoing pandemic. Discuss lineage and clade assignment and how we keep up to date with new versions of these.Clarify the changes needed to the underlying code for ARTIC analysis to accommodate midnight and,. ![]() I wanted to write a blog post about SARS-CoV-2 sequencing data analysis to achieve two things: ![]()
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