GB-eaSy

GB-eaSy processes genotyping-by-sequencing (GBS) short-read data to call single nucleotide polymorphisms (SNPs) and genotype samples from complex, including polyploid, crop genomes for genomics analyses.

Key Features:

• GBS data processing: Processes restriction-enzyme reduced-representation fragments generated on short-read sequencing platforms for downstream analysis.
• Polyploid support: Tailored for analysis of complex and polyploid genomes, including duplicated crop genomes.
• Parallelization and automation: Integrates widely used genomics tools with parallelization and automation for scalable processing.
• Low-coverage Illumina evaluation: Evaluated on low-coverage Illumina sequence data from soybean populations.
• SNP discovery and concordance: Performs SNP discovery and variant calling with high yield and concordance to whole-genome sequencing (WGS) in tested datasets.
• Efficiency: Optimizes run time and disk space usage during analysis.
• Modular open-source composition: Built from existing open-source, modular software packages.
• Complementary call sets: Produces SNP call sets that are largely complementary to other GBS workflows despite low convergence across platforms.

Scientific Applications:

• Variant discovery and genotyping: Identify genetic variants and genotype samples from GBS data, including single nucleotide polymorphisms (SNPs).
• Crop and polyploid genomics: Analyze genomic variation in complex and polyploid crop species, exemplified by soybean populations.
• Low-coverage sequencing studies: Enable population-genomic analyses using low-coverage Illumina sequencing data.
• Pipeline benchmarking and integration: Compare GBS bioinformatics pipelines and integrate results from multiple workflows to maximize SNP yield and accuracy.

Methodology:

Integrates existing open-source genomics tools with parallelization and automation to process restriction-enzyme reduced-representation short-read (Illumina) GBS data for SNP and genotype calling, with evaluation by comparison of SNP calls to whole-genome sequencing.