Welcome to GTG SARS-CoV-2 docs

Here is the documentation for running SARS-CoV-2 amplicons through nanopore sequencing to get consensus genomes and find their lineages.

Most of the information here is tested thoroughly with the Eden 2.5kb amplicon system, using the rapid barcoding kits, on PromethION flowcells. Most people will be using something else, and we recommend using the Midnight 1.2kb amplicons, or artic V3 amplicons.

Parts of the pipelines must be modified for use with the appropriate amplicon scheme. We have tried to make it clear where in the processes these changes need to be implemented, along with some tips along the way.

Please let us know if you have any questions, or require assistance.

Publication: Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

Pre-print: Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

Git-hub: SARS-CoV-2_GTG

Nanopore: Oxford Nanopore Technologies

RAMPART: artic-network/rampart

ARTIC (300bp): nCoV-2019 sequencing protocol v3 (LoCost) V.3

Midnight (1200bp): nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon) V.4

Eden (2500bp): SARS-CoV-2 Genome Sequencing Using Long Pooled Amplicons on Illumina Platforms