This is a demonstration of the use of Binder and github for reproducible research.
The binder can be accessed by clicking on the 'Launch binder' badge above. This binder will launch the ipython notebook demoReplaceReads.ipynb that will demonstrate the insertion of indels from one read (e.g. from amplicon sequencing of a CRISPR/Cas9 experiment) into other reads (e.g. a whole genome sequencing sample). Also included in the ipython notebook is an example of using Pindel to discover simulated reads and a plot showing the rate of simulation vs recovery using pindel.