Can't say about R packages but artemis, ncbi genome workbench, IGV, UCSC genome browser etc are some among popular and frequently used.

UCSC website (http://genome.ucsc.edu) has some very powerful tools in addition to its genome browser with lot of optional track and the possibility to view your own data aligned to databases, and a table browser with which you can download the data you see.

all the best

fred

Frederic Lepretre, Abhijeet Singh , thank you very much!

Yes, I know the specific software that is capable for creating such illustrations - in fact I frequently use SnapGene Viewer or UGENE to make simple maps of a single gene.

But since I work with R a lot and the results are usually in a form of Granges objects - it would be much more convenient to use some R package. And SnapGene can't show the read coverage, on the other hand - UGENE can show read coverage but can't combine it with the view of genomic features

Hi Igor

in UCSC you have the possibility to map your own data (reads for example) in front of many data in this tool. you can also export the view in vectorial pdf, which is very fine.

try an see

all the best

fred

Found the solution:

I use gggenes package to plot the genomic features, map reads using plotBed() of the sushi package and then combine the plots together in pdf-editor.

Unfortunatelly, the plots are uncombinable using R.