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!
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)