Updated: 2013 November 15th A while ago I asked on Twitter, what are some tools that people use to visualise hundreds of bam files. One of the suggestions was Gviz (thanks Sebastian!) and I had a quick glimpse at the Bioconductor package and the plots looked really great! Here I use Gviz to plot features along a reference sequence and for visualising bam files. From the vignette: The Gviz package