MindTheGap v2.0.0 has just been released !
MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome (See the web page). After a long period with few developments (publication in 2014), the whole code of MindTheGap was refactored to use the GATB library. Therefore MindTheGap became faster and easier to use. In addition, novel features have been implemented that improve also the results quality. Have a look at a comparison between the published and the 2.0.0 versions on simulated data here.
Inria
IRISA