generating draft genome

Question

[dranasnio]

Hi, 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?

Answer 1

[lieven.sterck]

typically you will need another level of information about your genome.

Classic approach is to include genetic maps which , based on marker alignment, can assign scaffolds to linkage groups/pseudo-chroms.

Nowadays, you can also go for HiC or other contact data (10x for instance).

(in your specific case, if your species has 12 chromos you're already nearly there)

Answer 2

[oschwengers]

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".

pros:

• clearly artificial, searchable and identifiable
• no artificial genes called due to the "TAG" stop codons on each of the 6 reading frames