REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

Marchet, Camille; Iqbal, Zamin; Gautheret, Daniel; Salson, Mikaël; Chikhi, Rayan

Document type :

Article dans une revue scientifique

DOI :

10.1093/bioinformatics/btaa487

PMID :

32657392

Title :

REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

Author(s) :

Marchet, Camille [Auteur correspondant]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Iqbal, Zamin [Auteur]
Gautheret, Daniel [Auteur]
Institut de Biologie Intégrative de la Cellule [I2BC]
Salson, Mikaël [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Chikhi, Rayan [Auteur]

Algorithmes pour les séquences biologiques - Sequence Bioinformatics

Journal title :

Bioinformatics

Pages :

i177-i185

Publisher :

Oxford University Press (OUP)

Publication date :

2020-07-01

ISSN :

1367-4803

HAL domain(s) :

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

English abstract : [en]

MotivationIn this work we present REINDEER, a novel computational method that performs indexing of sequences and records their abundances across a collection of datasets. To the best of our knowledge, other indexing methods ...
Show more >MotivationIn this work we present REINDEER, a novel computational method that performs indexing of sequences and records their abundances across a collection of datasets. To the best of our knowledge, other indexing methods have so far been unable to record abundances efficiently across large datasets.ResultsWe used REINDEER to index the abundances of sequences within 2585 human RNA-seq experiments in 45 h using only 56 GB of RAM. This makes REINDEER the first method able to record abundances at the scale of ∼4 billion distinct k-mers across 2585 datasets. REINDEER also supports exact presence/absence queries of k-mers. Briefly, REINDEER constructs the compacted de Bruijn graph of each dataset, then conceptually merges those de Bruijn graphs into a single global one. Then, REINDEER constructs and indexes monotigs, which in a nutshell are groups of k-mers of similar abundances. Availability and implementation https://github.com/kamimrcht/REINDEER. Supplementary information Supplementary data are available at Bioinformatics online.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

ANR Project :

Signatures transcriptionnelles pour une analyse RNA-seq globale
Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs

Collections :

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

Source :

Harvested from HAL

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