Tool: MindTheGap new release !
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gravatar for claire.lemaitre
9 months ago by
France
claire.lemaitre100 wrote:

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 ?

Claire Lemaitre and Guillaume Rizk

tool gatb mindthegap • 294 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by claire.lemaitre100
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