The TASSEL-GBS pipeline is a bioinformatics tool designed for efficient processing of raw genotyping by sequencing (GBS) data into SNP genotypes. It is designed to run on modest computing resources, handle large-scale studies with hundreds of thousands or even millions of SNPs in up to 100,000 individuals, and support accelerated breeding contexts. The pipeline can be run with a reference genome or an incomplete "pseudo-reference" consisting of numerous contigs. The authors describe the TASSEL-GBS pipeline in detail and benchmark it using a large-scale, species-wide analysis in maize (Zea mays), achieving an average error rate of 0.0042 through the application of population genetic-based SNP filters. The TASSEL-GBS pipeline provides robust tools for studying genomic diversity and is particularly useful for high-throughput, accelerated plant breeding.The TASSEL-GBS pipeline is a bioinformatics tool designed for efficient processing of raw genotyping by sequencing (GBS) data into SNP genotypes. It is designed to run on modest computing resources, handle large-scale studies with hundreds of thousands or even millions of SNPs in up to 100,000 individuals, and support accelerated breeding contexts. The pipeline can be run with a reference genome or an incomplete "pseudo-reference" consisting of numerous contigs. The authors describe the TASSEL-GBS pipeline in detail and benchmark it using a large-scale, species-wide analysis in maize (Zea mays), achieving an average error rate of 0.0042 through the application of population genetic-based SNP filters. The TASSEL-GBS pipeline provides robust tools for studying genomic diversity and is particularly useful for high-throughput, accelerated plant breeding.