How to find the coverage of the assembled contigs of the PacBio long reads?

Question

[rj.rezwan]

Hi, I have assembled the 3-cells reads data of PacBio HiFi. Question is how can I find the coverage of my assembled contigs? I shall be grateful to you.

Answer 1

[liorglic]

Depends on what you mean by "coverage of contigs".
If you want to know how many of your reads support each contig, then you can simply map your reads to the assembled contigs (e.g. using minimap2) and analyze the mapping results (e.g. using samtools).
If what you mean is the fraction of the genome covered by contigs, then you can:
(1) Map your contigs to a relevant reference genome, if one exists, and see how much of it is covered.
(2) If no reference exists, you can obtain some other estimate of the genome size by performing a k-mer analysis or based on flow cytometry. Then compare it to your assembly size.

[rj.rezwan]

Hi, I caculated the coverage by mapping the assembled contigs with the reads of pacbio hifi. the output bam file is used for samtools using coverage function in it. I finally found the average coverage 92.13. is it good one in long reads assembly?

[liorglic]

It sounds like decent coverage, but this does not really tell you that much if you want to assess the quality of your assembly. To do that, you can calculate things like the % of genome assembled (compared to the expected size), N50, and % BUSCOs.