Coronavirus Resources

Assembling SARS-CoV-2 Genomes

A workflow for assembly of SARS-CoV-2 sequences from Illumina data, including quality trimming and removal of amplicon primers, map to reference, SNP calling and consensus generation.

Assembly of SARS-CoV-2 genomes from tiled amplicon Illumina sequencing using Geneious Prime

Betacoronavirus BLAST

NCBI has a new BLAST database for betacoronaviruses. To add this database to the Geneious NCBI BLAST, go to Tools -> Add/Remove Databases ->Set up BLAST Services. Under the NCBI tab, click Edit Databases, and then Add+. Enter the details as in the screenshot – ensure the database name is written exactly as shown here.

Geneious Prime Formatted Files for SARS-CoV-2

1. SARS-CoV-2 Reference Genome

MN908947.geneious

2. Artic Network Primers for Tiled Amplicon Sequencing

Sars-CoV-2 V3 primers for tiled amplicon sequencing from the Artic Network

Artic V3 primers.geneious

Further information on importing other amplicon primer sets – Quick guide to importing primer sets from TSV/CSV files

3. WHO Primers and Probes for the SARS-CoV-2 Genome

(List assembled by Martin Reijns at the MRC Human Genetics Unit at the University of Edinburgh.)

SARS-Cov-2 Primers & Probes.geneious

4. SARS-CoV-2 Genomes from NCBI Viruses

(All nucleotide sequences available on the NCBI SARS-CoV-2 data hub as at 12th May 2020)

SARS-CoV-2 Genbank sequences.geneious

To update this list with new sequences as they are released, we recommend setting up an Agent.  To do this, go to View -> Agents, then click Create.  Select Nucleotide under Search Database, and search by Organism contains “Severe acute respiratory syndrome coronavirus 2”, as shown in the screenshot below.

Note that there is a delay of a few days between a sequence appearing on the NCBI SARS-CoV-2 data hub and being available for searching in NCBI Nucleotide.