Protocols

SARS-CoV-2 sequencing using ARTIC PrimalSeq-LibAmp
By: Catie Anderson, Mark Zeller

Updated protocol for sequencing SARS-CoV-2 using a shorter amplicon scheme for PrimalSeq. The average length of amplicons in this protocol is ~250 nt, making this well-suited to sequencing on NovaSeq, iSeq, and NextSeq platforms.

SARS-CoV-2 sequencing using ARTIC PrimalSeq-Nextera
By: Catie Anderson, Mark Zeller

Protocol for sequencing SARS-CoV-2 using ARTIC PrimalSeq. The average length of amplicons in this protocol is ~400 nt, making this well-suited to sequencing on the MiSeq.

MiSeq protocol for PrimalSeq/ARTIC virus sequencing with contamination control
By: Nate Matteson, Nate Grubaugh, Karthik Gangavarapu, Josh Quick, Nick Loman, Kristian Andersen

This is an easy-to-follow protocol (“PrimalSeq”) that uses “PrimalScheme”-based amplicon sequencing of virus genomes directly on the Illumina platform. In this updated version, we use spike-ins to control for cross-sample contamination.

COVID-19 screening using CDC and WHO primers
By: Catie Anderson, Mark Zeller

Protocol for COVID-19 screening using CDC and WHO primers.

Zika virus plaque assay
By: Glenn Oliveira

This is an easy-to-follow protocol for creating a plaque assay for Zika virus using crystal violet for easy counting.

Lassa virus sequencing
By: Matthias Pauthner

This is an easy-to-follow protocol for high-coverage sequencing of Lassa virus S Segments.

MinION protocol for Zika virus sequencing
By: Josh Quick, Nick Loman, Team ZiBRA

This is an easy-to-follow protocol that uses “PrimalScheme”-based amplicon sequencing of Zika virus genomes directly on the MinION platform.