Mobster is a tool written in Java which can detect non-reference mobile element (transposon) insertions in next generation sequencing data.
Mobster works on BAM files as input and uses both discordant and split reads to detect mobile element insertions (MEIs). Discordant reads and split reads are mapped to a database of consensus sequences of active mobile elements. When multiple reads, originating from the same genomic region are aligned to the same mobile element family a potential insertion has been found.
For more detailed information, please read our Genome Biology article