evaluation of sequencing coverage depth

Question

[piotr.majewski]

Dear All,

At the outset, I would like to point out that I am an amateur in the field of NGS.

I've performed sequencing of prokaryotic genome (Alcaligenes faecalis with use of short (Illumina) and long reads (Nanopore). My goal is to fully resolve genome and mobilome structures with use of hybrid assembly (Unicycler).

Here comes the stupid question - how can I determine coverage depth? I should check FASTQ/FAST5 from both technologies separately?

thanks in advance,

Piotr

[GenoMax]

You can align your reads back to the assembly you have (referred to in a separate question). That should allow you to check depth at every base (use mosdepth or samtools depth) using the alignment files you get. Use minimap2 for alignment with long reads and any other NGS aligner for Illumina short reads.