PAC (Partitionned Aggregated bloom Comb trees)

Camille Marchet (1) , Antoine Limasset (2, 1)

1 CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189
2 CNRS - Centre National de la Recherche Scientifique

PAC is a scalable structure able to list datasets that may contain a query sequence among thousands of indexed files. PAC is an AMQ (Approximate membership Query) structure based on bloom filters like Cobs, or Sequence Bloom tree tools (HowDeSBT,AllsomeSBT,SSBT,...) A PAC index can be built from thousands datasets quickly and with low resource memory and disk footprint and can deliver very high query throughput.

Mots clés: AMQ; Data structure; K-mer; Pangenomics

Domaines: Algorithme et structure de données [cs.DS]; Génomique, Transcriptomique et Protéomique [q-bio.GN]

Camille Marchet, Antoine Limasset. PAC (Partitionned Aggregated bloom Comb trees). 2021, ⟨swh:1:dir:71df7ad3c1d66b4989702820283a7cc3e9bfd5e5;origin=https://hal.archives-ouvertes.fr/hal-04441806;visit=swh:1:snp:5e96275dff1a0983e64f36993e8cfa6a2bf4ee9b;anchor=swh:1:rel:9d59c913641e1e548439d22aced030ded561a90e;path=/⟩. ⟨hal-04441806⟩