diagno-syst: a tool for accurate inventories in metabarcoding

Abstract : Metabarcoding on amplicons is rapidly expanding as a method to produce molecular based inventories of microbial communities. Here, we work on freshwater diatoms, which are microalgae possibly inventoried both on a morphological and a molecular basis. We have developed an algorithm, in a program called diagno-syst, based a the notion of informative read, which carries out supervised clustering of reads by mapping them exactly one by one on all reads of a well curated and taxonomically annotated reference database. This program has been run on a HPC (and HTC) infrastructure to address computation load. We compare optical and molecular based inventories on 10 samples from Léman lake, and 30 from Swedish rivers. We track all possibilities of mismatches between both approaches, and compare the results with standard pipelines (with heuristics) like Mothur. We find that the comparison with optics is more accurate when using exact calculations, at the price of a heavier computation load. It is crucial when studying the long tail of biodiversity, which may be overestimated by pipelines or algorithms using heuristics instead (more false positive). This work supports the analysis that these methods will benefit from progress in, first, building an agreement between molecular based and morphological based systematics and, second, having as complete as possible publicly available reference databases.
Type de document :
Pré-publication, Document de travail
2016
Liste complète des métadonnées

https://hal.inria.fr/hal-01426764
Contributeur : David James Sherman <>
Soumis le : mercredi 4 janvier 2017 - 20:15:05
Dernière modification le : mardi 17 avril 2018 - 09:04:28
Document(s) archivé(s) le : mercredi 5 avril 2017 - 15:26:54

Fichier

1611.09410v1.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

  • HAL Id : hal-01426764, version 1
  • ARXIV : 1611.09410

Collections

Citation

Jean-Marc Frigerio, Frédéric Rimet, Agnès Bouchez, Emilie Chancerel, Philippe Chaumeil, et al.. diagno-syst: a tool for accurate inventories in metabarcoding. 2016. 〈hal-01426764〉

Partager

Métriques

Consultations de la notice

319

Téléchargements de fichiers

52