Generate single genome consensus fasta file from SPAdes output: viral genome sequencing

Question

[snow_seq]

I am assembling a viral genome of 30kb de novo using SPAdes. I have fasta files for scaffolds and contigs. How do I process these into one final genome sequence, i.e. one fasta file with one sequence? What softwares are there for doing this? I would like to do pairwise alignment with published viral genome sequences from other labs/sources.Thanks in advance!

Answer 1

[Asaf]

The contigs file you have are the best the algorithm could do in assembling the genome. The scaffolds are contigs stitched together using paired-end data and some guessing about the insert size. I'm surprised you didn't get the entire genome in one contig. Do you have a reference to compare to? (my guess is you have thousands by now)

[snow_seq]

Hi, thanks for your reply! Yes, I'm sequencing SARS-CoV-2. My largest contig is about 3kb and all scaffolds/contigs only cover only about 85-90% of the genome. Before assembly, I trimmed adapters and primers and normalizedto a depth of 100X. The per nucleotide coverage looked fine before assembly and after normalization, so I'm not quite sure why I am getting poor assembly results.

[Asaf]

Maybe take a look at the assembly graph. Also, you can do amplicon sequencing: https://eu.idtdna.com/pages/landing/coronavirus-research-reagents/ngs-assays