I have recently analyzed my metagenomic data using the metagenome-atlas. I have a set of MAGs of varying completeness/contamination and from different lineages and am looking for a way to visualize the coverage.
I have previously used BRIG before but not for coverage mapping, but I am aware that it does have a coverage mapping module. However, I am confused as to what my reference data would be.
I have also had some R packages recommended to me by colleagues (ggbio, circlize) but have no experience using these.
Any suggestions on what to use? Unfortunately I only have the atlas outputs because I do not have access to a server which can operate metagenome-atlas anymore.