Skip to Main content Skip to Navigation
Preprints, Working Papers, ...

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.
Document type :
Preprints, Working Papers, ...
Complete list of metadata
Contributor : David James Sherman Connect in order to contact the contributor
Submitted on : Wednesday, January 4, 2017 - 8:15:05 PM
Last modification on : Tuesday, June 14, 2022 - 8:25:48 AM
Long-term archiving on: : Wednesday, April 5, 2017 - 3:26:54 PM


Files produced by the author(s)


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


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



Record views


Files downloads