Two read mapping formats are supported: reads tracks and stand-alone read mappings. As a basic overview:
- Reads tracks
- are designed for viewing alongside other results that are based on the same reference genome coordinates, using a Track List. Most NGS-related analysis functionality has been implemented using tracks, taking advantage of the consistent coordinate system.
- Stand-alone read mappings
- provide rich visualization and editing features. They contain features such as a consensus sequence and coverage graph and can thus be useful when working with a particular read mapping in detail. Further details about working with stand alone read mappings can be found in View and edit read mapping.
Read mappings can be converted from stand-alone to reads tracks or vice versa as described in Converting data to tracks and back.
In this section, we describe the meaning of the default coloring of reads in read mappings Coloring of mapped reads, the features of reads tracks Reads tracks and the features of stand-alone read mappings Stand-alone read mapping.