Hi! I have a few sets of multiple fasta files (mostly genes and huge set of markers) in .fasta formatted with only name tags (no separated description or something) and genome sequence in multiple fasta .fa file (it's formatted similarly as previous as 21 superscaffolds/chromosomes). I also have BLAST files for all the sets against genome in few formats (also tabular/CSV). So I have this genome and all the sequences with corresponding hits, but I'm struggling how to map them on the genome(visualy display as map which will correspond to sequences lenghts). I was already trying few programs but I'm challenging some problems with data size or format. I think there need to be something which can display that data and I was thinking on using R but I'm a newbie and I don't really know how. I'm hoping for your help and suggestion.
You could try BRIG, as it literally displays blast hits against a reference sequence, somewhat like circos.
If you're happy working in Python too, I quite like BioGraPy http://apierleoni.github.io/BioGraPy/
It's still in development though so may not entirely do what you need.