A bioinformatics pipeline designed for the efficient processing of raw GBS sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished "pseudo-reference" consisting of numerous contigs.
A software application designed to analyze and report results of genotyping-by-sequencing. Haplotag operates with minimal user-investment on widely-available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode and a production mode; (4) discovers polymorphisms based on a model of local haplotypes within sequenced tags; (5) reports SNPs as well as haplotype-based genotypes; (6) provides an intuitive visual “passport” for each inferred locus.
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