for a reference guided denovo assembly, how can we generate a pseudocontig(as in contiguator) from the scaffolds generated from medusa? ie, I have a scaffold.fasta with 12 scaffolds. i need to convert it as a single draft genome. how it can be done?
If you'd like to come up with an artificial single-molecule genome, we used to concatenate the ordered and scaffolded contigs (against a closely-related finished genome) using an artificial 6-frame stop linker: "NNNNNNNNNNCTAGCTAGCTAGCNNNNNNNNNN".
clearly artificial, searchable and identifiable
no artificial genes called due to the "TAG" stop codons on each of the 6 reading frames