v2.3.0

Improving the Find (insertion breakpoint finder) module:

• very small insertions (1 or 2 bp) are now directly assembled in the Find module and are output in the .othervariants.vcf file. This may increase the running time of the Find module but the overall running time of MindTheGap (Find+Fill) is drastically reduced. Indeed, these numerous small insertions are no longer output in the breakpoint file, nor given as input for the Fill assembly module which performs a deeper traversal of the de Bruijn graph (designed for longer insertions).
• a novel filter is implemented to reduce the amount of False Positive insertion sites. It is based on the number of branching kmers in a 100-bp window before a heterozygous site. It can be tuned with the novel option -branching-filter. It is now activated by default, so this may modify the amount of heterozygous sites detected with respect to previous versions.

With this new version, the running time of MindTheGap as an insertion variant caller is reduced for real large datasets, such as human genome re-sequencing data.