A reference sequence for assembling your viral genome sequencing reads can be downloaded directly from NCBI during project set up.

From the Reference Sequence step, click on Download NCBI Genomes, then either browse available genomes, or enter the accession number for the genome you wish to download.

To access the viral genome sequencing analysis workflow, first launch SeqMan Ultra and choose New Assembly.  Then, choose from one of the following:

1. If you have long read data from Oxford Nanopore or PacBio, choose ARTIC amplicon under the Genomics section.
2. If you have short read NGS data from Illumina or Ion Torrent, choose Variant analysis and resequencing under the Genomics section, then choose NGS-Based > Whole Genome from the resulting SeqMan NGen wizard.
3. If you have Sanger/ABI data, choose Variant analysis and resequencing under the Genomics section, then choose ABI/Sanger > Whole Genome from the resulting SeqMan NGen wizard.

You can align the consensus sequences for your assembled reads to known viral strains using MegAlign Pro. To do this, first export your consensus sequences from SeqMan Ultra by selecting File > Export Data > Consensus. Then, add these exported consensus sequences to MegAlign Pro along with known strains (publicly available from NCBI). After adding all of the sequences you wish to align, select Align > Align Using MAFFT.

If you are starting with raw, unassembled reads, you will need Lasergene Genomics to assemble your sequencing data and generate consensus sequences. You will need Lasergene Molecular Biology to access MegAlign Pro for aligning your assembled genomes to known strains and identifying variants. Both Lasergene Genomics and Lasergene Molecular Biology are included in the full DNASTAR Lasergene package. If you already have draft genomes that you wish to align to known strains, then you will only need the Lasergene Molecular Biology package.