MindTheGap is a tool to detect and assemble insertion variants of any size and any type, by comparison with a reference genome.
For download and more details, see the web page : https://gatb.inria.fr/software/mind-the-gap/
Guillaume Rizk, Anaïs Gouin, Rayan Chikhi and Claire Lemaitre. MindTheGap : integrated detection and assembly of short and long insertions. Bioinformatics 2014 (on line 10.1093/bioinformatics/btu545 August 14, 2014).
See also the poster, presented at ECCB’14 : pdf