MindTheGap is a tool specifically designed to assemble insertion variants from re-sequencing data. It implements an algorithm that performs the following three stages: (i) creating de Bruijn graph from short read data (ii) detection of insertion breakpoints in a given reference genome, and (iii) local assembly of the inserts.
Rizk G, Gouin A, Chikhi R, Lemaitre C "MindTheGap: integrated detection and assembly of short and long insertions." Bioinformatics. 2014 Dec 15;30(24):3451-7. Epub 2014 Aug 14. https://doi.org/10.1093/bioinformatics/btu545
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