supersampler Fractionnal hitting set implementation for lightweight genomic data sketching
Résumé
Bird-eye view
SuperSampler (SPSP) is an implementation for a novel k-mer selection scheme we called Fractional Hitting Sets (FHS) which is a generalisation of Universal Hitting Sets (UHS). It allows to quickly create sketches of genomes/ metagenomes and to compare such sketches to obtain Containment or Jaccard indices of the input data.
SuperSampler uses super-k-mers instead of k-mers which allows for lighter sketches, less RAM usage and less computational time when performing comparison than traditional subsampling methods. Thanks to a clever sketch organisation allowed by the super-k-mers structure.
Sketch creation is an application of FracMinHash on the selection of minimizers (a m-mer of a k-mer which hash value is minimal). When a minimizer is selected, every k-mer around it which shares the same minimizer is selected and will form a super-k-mer.
