Software: MindTheGap

Detection and assembly of insertion variants


MindTheGap is a software that performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.

It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detected insertion sites, the other is the set of assembled insertions for each breakpoint. For each breakpoint, MindTheGap either returns a single insertion sequence (when there is no assembly ambiguity), or a set of candidate insertion sequences (due to ambiguities) or nothing at all (when the insertion is too com- plex to be assembled).

MindTheGap performs de novo assembly using Minia. Hence, the computational resources required to run MindTheGap are significantly lower than that of other assemblers.

Here is a poster presenting the method and some results on simulated and real data.


Sources and binaries are available:


Get the manual here.



Guillaume Rizk, Anaïs Gouin, Rayan Chikhi and Claire Lemaitre. MindTheGap: integrated detection and assembly of short and long insertions. Bioinformatics 2014 (advance access)


Any comments or suggestions are warmly welcome. Don’t hesitate to send an email to claire-dot-lemaitre-at-inria-dot-fr

[Last modified August, 25, 2014]