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.
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.
2. Artic Network Primers for Tiled Amplicon Sequencing
Sars-CoV-2 V3 primers for tiled amplicon sequencing from the Artic Network
Further information on importing other amplicon primer sets – Quick guide to importing primer sets from TSV/CSV files
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)
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.