I came across some literature where people have used IDBA-UD to perform a scaffolding step on assembled contigs from other assemblers such as MEGAHIT.
I am thinking of using the following code
idba \ --read merged_raw_reads.fa \ --read_level_2 megahit_contigs.fa \ --out idba_scaffolds.fa
But I am not sure how it's supposed to be done from reading the IDBA-UD manual, could someone help with this? Much appreciated!