DiscoSnp-RAD: de novo detection of small variants for population genomics

Abstract

Abstract. We present an original method to de novo call variants for Restriction site associated DNA Sequencing (RAD-Seq). RAD-Seq is a technique characterized by the sequencing of specific loci along the genome, that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, as STACKS or IPyRAD, are based on all-versus-all read comparisons, which require consequent time and computing resources. Based on the variant caller DiscoSnp, initially designed for shotgun sequencing, DiscoSnp-RAD avoids this pitfall as variants are detected by exploring the De Bruijn Graph built from all the read datasets. We tested the implementation on RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions. Furthermore, our results show that DiscoSnp-RAD is at least one order of magnitude faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD data, and stands out from other tools due to his completely different principle, making it significantly faster, in particular on large datasets.

Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

“…First, sequencing primers were removed, sequences were demultiplexed and associated with each individual based on internal barcode sequences. SNP‐calling was performed on samples from each species separately using DiscoSnp‐RAD, a de novo reference‐free and assembly‐free method (Gauthier et al, 2017; Uricaru et al, 2015). SNPs are identified from particular arrangements in the De Bruijn graph built using a k‐mer size of 31 and a minimal coverage of two for each allele (Gauthier et al, 2017; Uricaru et al, 2015).…”

“…SNP‐calling was performed on samples from each species separately using DiscoSnp‐RAD, a de novo reference‐free and assembly‐free method (Gauthier et al, 2017; Uricaru et al, 2015). SNPs are identified from particular arrangements in the De Bruijn graph built using a k‐mer size of 31 and a minimal coverage of two for each allele (Gauthier et al, 2017; Uricaru et al, 2015). Individuals with more than 90% missing genotypes were excluded (Table ) resulting in a final data set consisting of 105 samples for I. salapia and 142 for O. onega .…”

Genome-wide diversity of coconut from northern South America uncovers genotypes present in Colombia and strong population structure

“…FastQC reports (Andrews, 2008) were 192 prepared for all FASTQ files and read counts were recorded. Two software were implemented to call variants for the pilot study with the goal of finding the 194 best performing program: DiscoSnpRad (Gauthier et al, 2017), and Stacks (Catchen et al, 195 2013). The best performing restriction enzyme and best bioinformatics pipelines to call variants 196 were subsequently used for this study (Table S2) Other parameters were left as default.…”