title: Reference-free detection of isolated SNPs.
abstract: Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, discoSnp, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, discoSnp ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, discoSnp requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives. An experimental validation was conducted on an arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs that were tested, 96% were successfully genotyped and truly exhibited polymorphism.
authors.affiliation: University of Bordeaux, CNRS/LaBRI, F-33405 Talence, France University of Bordeaux, CBiB, F-33000 Bordeaux, France INRA, UMR1349 IGEPP, Le Rheu, France ruricaru@labri.fr.
authors.forename: Raluca
authors.initials: R
authors.lastname: Uricaru
authors.affiliation: GenScale, INRIA Rennes Bretagne-Atlantique, IRISA, Rennes, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Rizk
authors.affiliation: BAMBOO, INRIA Grenoble Rhone-Alpes, Lyon, France Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1 UMR CNRS 5558, Lyon, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Lacroix
authors.affiliation: INRA, UMR1300 Biology, Epidemiology and Risk Analysis in Animal Health, Nantes, France LUNAM University, Oniris, Nantes Atlantic College of Veterinary Medicine and Food Sciences and Engineering, UMR BioEpAR, Nantes, France.
authors.forename: Elsa
authors.initials: E
authors.lastname: Quillery
authors.affiliation: INRA, UMR1300 Biology, Epidemiology and Risk Analysis in Animal Health, Nantes, France LUNAM University, Oniris, Nantes Atlantic College of Veterinary Medicine and Food Sciences and Engineering, UMR BioEpAR, Nantes, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Plantard
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.
authors.forename: Rayan
authors.initials: R
authors.lastname: Chikhi
authors.affiliation: GenScale, INRIA Rennes Bretagne-Atlantique, IRISA, Rennes, France claire.lemaitre@inria.fr.
authors.forename: Claire
authors.initials: C
authors.lastname: Lemaitre
authors.affiliation: GenScale, INRIA Rennes Bretagne-Atlantique, IRISA, Rennes, France pierre.peterlongo@inria.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peterlongo
mesh_terms: D000465:Algorithms; D000818:Animals; D002878:Chromosomes, Human, Pair 1; D004926:Escherichia coli / Q000235:genetics; D023281:Genomics / Q000379:methods; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D018884:Ixodes / Q000235:genetics; D051379:Mice; D008810:Mice, Inbred C57BL; D020641:Polymorphism, Single Nucleotide; D012441:Saccharomyces cerevisiae / Q000235:genetics