Dear MindTheGap enthusiasts,

What is MindTheGap?

MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. It is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.

See the initial publication:

MindTheGap: integrated detection and assembly of short and long insertions. Guillaume Rizk, Anaïs Gouin, Rayan Chikhi and Claire Lemaitre. Bioinformatics, 2014, 30(24):3451-3457.

What's new in this release (v2.0.0)?

• This is the first release after refactoring the whole code of MindTheGap to use the GATB library. Some of the benefits:
  • faster (thanks to GATB improvements in kmer counting!);
  • no longer need to recompile for changing the k parameter;
  • automatic estimation of the paramater abundance-min;
  • more user-friendly usage, with more readable help, progress bars, input-output summaries, etc.
  • compatibility with other GATB tools: input-output graph in h5 format.
• New features (with respect to the published version, August 2014):
  • detection of homozygous SNPs and deletions (output in a separate VCF file); this should also improve the recall of insertion event detection;
  • a quality score is now associated to each insertion prediction, this enables to filter out some predictions and to obtain a high-confidence subset.

Have a look at a comparison between the published and the 2.0.0 versions on simulated data here.

How to get MindTheGap?

• On github: https://github.com/GATB/MindTheGap
• Web site: https://gatb.inria.fr/software/mind-the-gap/

Claire Lemaitre and Guillaume Rizk