Robust and efficient software for reference‐free genomic diversity analysis of genotyping‐by‐sequencing data on diploid and polyploid species

Abstract

Genotyping-by-sequencing (GBS) is a widely used and cost-effective technique for obtaining large numbers of genetic markers from populations by sequencing regions adjacent to restriction cut sites. Although a standard reference-based pipeline can be followed to analyse GBS reads, a reference genome is still not available for a large number of species. Hence, reference-free approaches are required to generate the genetic variability information that can be obtained from a GBS experiment.Unfortunately, available tools to perform de novo analysis of GBS reads face issues of usability, accuracy and performance. Furthermore, few available tools are suitable for analysing data sets from polyploid species. In this manuscript, we describe a novel algorithm to perform reference-free variant detection and genotyping from GBS reads. Nonexact searches on a dynamic hash table of consensus sequences allow for efficient read clustering and sorting. This algorithm was integrated in the Next Generation Sequencing Experience Platform (NGSEP) to integrate the state-of-theart variant detector already implemented in this tool. We performed benchmark experiments with three different empirical data sets of plants and animals with different population structures and ploidies, and sequenced with different GBS protocols at different read depths. These experiments show that NGSEP has comparable and in some cases better accuracy and always better computational efficiency compared to existing solutions. We expect that this new development will be useful for many research groups conducting population genetic studies in a wide variety of species.

Rapid evolution of competitive ability in giant foxtail (Setaria faberi) over 34 years

“…The clean sequencing data were then used for further downstream processing. We used the DeNovoGBS module in NGSEP v. 4 software for individual read mapping and SNP mining (Parra-Salazar et al 2022). The NGSEP v. 4 software analysis called a total of 526,550 SNPs.…”

Seascape Genomics Reveals Metapopulation Connectivity Network of Paramuricea biscaya in the Northern Gulf of Mexico

“…We performed read clustering and single nucleotide polymorphism (SNP) calling using the DeNovoGBS (Parra-Salazar et al, 2021) module of the software package NGSEP v4.0.1 (Tello et al, 2019). This software is more computationally efficient and has comparable or better accuracy than programs like Stacks or pyRAD (Eaton, 2014) for de novo analysis of genotype-by-sequencing data (Parra-Salazar et al, 2021). We assumed a heterozygosity rate of 1.5% (-h 0.015) as calculated from the short read genome-wide data of the sister species Paramuricea sp.…”

Seascape genomics reveals metapopulation connectivity network of Paramuricea biscaya in the northern Gulf of Mexico

“…We de-multiplexed and quality filtered raw sequence RAD-seq reads using the process_radtags program in Stacks v2.1 (Catchen et al, 2013) with the following flags: --inline_null, -r, -c, and -q, with default values. We performed read clustering and single nucleotide polymorphism (SNP) calling using the DeNovoGBS (Parra-Salazar et al, 2021) module of the software package NGSEP v4.0.1 (Tello et al, 2019). This software is more computationally efficient and has comparable or better accuracy than programs like Stacks or pyRAD (Eaton, 2014) for de novo analysis of genotype-by-sequencing data (Parra-Salazar et al, 2021).…”

“…We performed read clustering and single nucleotide polymorphism (SNP) calling using the DeNovoGBS (Parra-Salazar et al, 2021) module of the software package NGSEP v4.0.1 (Tello et al, 2019). This software is more computationally efficient and has comparable or better accuracy than programs like Stacks or pyRAD (Eaton, 2014) for de novo analysis of genotype-by-sequencing data (Parra-Salazar et al, 2021). We assumed a heterozygosity rate of 1.5% (-h 0.015) as calculated from the short read genome-wide data of the sister species Paramuricea B3 using the software GenomeScope v2.0 (Vurture et al, 2017) from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject number PRJNA574146 (Vohsen et al, 2020).…”