Logiciel Année : 2023

supersampler Fractionnal hitting set implementation for lightweight genomic data sketching

Timothé Rouzé
Igor Martayan
Camille Marchet

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.

Mots clés

HAL

Cite hal-04279798v1 Objet présenté à une conférence Timothé Rouzé, Igor Martayan, Camille Marchet, Antoine Limasset. Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching. 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023, Sep 2023, Houston, United States. ⟨10.4230/LIPIcs.WABI.2023.15⟩. ⟨hal-04279798⟩

Citer

Antoine Limasset, Timothé Rouzé, Igor Martayan, Camille Marchet. supersampler Fractionnal hitting set implementation for lightweight genomic data sketching. 2023, ⟨swh:1:dir:bb6dea99f95337e2bf26180f5242fa4b09b897f6;origin=https://hal.archives-ouvertes.fr/hal-04448163;visit=swh:1:snp:1f35ba3a6890c0ed7ca0e06e4662f5abc05db16c;anchor=swh:1:rel:42686bbd8658ab7a2a280c4dd46d8bd8223a0851;path=/⟩. ⟨hal-04448163⟩
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