How to identify gaps in a genome?

Question

[rj.rezwan]

Hi, I assembled the genome using PacBio HiFi reads and Hi-C reads. I want to know how can I identify the gaps in genome. Is there any good tool for this? I shall be grateful to you.

[GenoMax]

Find related genomes (preferably finished) from NCBI and align your own to get some idea of coverage. Run BUSCO on your genome to see if you have captured most of the gene content expected to be present.

[rj.rezwan]

GenoMax I have higher BUSCO than the previously published genome but I am looking to find the "NNNNNN" regions in my genome that exhibit the gaps.

Answer 1

[colindaven]

You can use seqtk to find gaps in a fasta

https://github.com/lh3/seqtk

seqtk gap
Usage: seqtk gap [-l 50] <in.fa>