IGV 2.0 integrates support for Goby NGS file formats.  Goby is an NGS data management framework designed to facilitate the implementation of efficient data analysis pipelines. It provides  efficient file formats to store NGS data and intermediary analysis results.

IGV 2.0.4 renders Goby alignments with lines connecting parts of reads that span exon-exon junctions. Alignments with splicing information can be generated for RNA-Seq data with GSNAP compiled with Goby support. Splicing information is automatically detected when present and displayed. See example here.

IGV supports Goby coverage data .counts files.

For more information on these file formats, see the Goby NGS Framework Web site. For details on current and planned Goby support in IGV see the IGV development wiki.