I have used bg seq for small-read sequencing of a fish's whole genome. I have used megahit and spades to assemble these genomes and have some contigs. can someone suggest a pipeline to get a chromosome-level assembly after this step?
Do you mean BGI-seq and short reads ? If so, you can't get to chromosomes from this start.
You'll need long pacbio or nanopore reads and a) a related reference genome and software like RagTag - https://github.com/malonge/RagTag or b) Hi-C reads to get to chromosome level.
There are literally thousands of examples of how to do this in the literature so please check related papers for details.
