supersamplerFractionnal hitting set implementation for lightweight genomic data sketching

Limasset, Antoine; Rouzé, Timothé; Martayan, Igor; Marchet, Camille

Document type :

Autre communication scientifique (congrès sans actes - poster - séminaire...)

Title :

supersamplerFractionnal hitting set implementation for lightweight genomic data sketching

Author(s) :

Limasset, Antoine [Auteur]

Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Centre National de la Recherche Scientifique [CNRS]
Rouzé, Timothé [Auteur]
Martayan, Igor [Auteur]
Marchet, Camille [Auteur]

English keyword(s) :

minimizers
indexing
kmers

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]

English abstract : [en]

Bird-eye viewSuperSampler (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 ...
Show more >Bird-eye viewSuperSampler (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.Show less >

Language :

Anglais

ANR Project :

Structures de graphe adaptées pour l'exploration de données de séquençage de troisième génération

Collections :

Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL

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