Welcome to the GBS-SNP-CROP pipeline forum

This discussion group provides an online source of information about the pipeline. The pipeline scripts and further information, as well as links to the original publication, can be found at the GBS-SNP-CROP Github page, https://github.com/halelab/GBS-SNP-CROP.git

The GBS SNP Calling Reference Optional Pipeline (GBS-SNP-CROP) is executed via a sequence of seven PERL scripts which integrate custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving the user full access to all intermediate files. By employing a novel strategy of SNP calling based on the correspondence of within- individual to across-population patterns of polymorphism, the pipeline is able to identify and distinguish high-confidence SNPs from both sequencing and PCR errors. GBS- SNP-CROP is a complete bioinformatics pipeline developed primarily to support curation, research, and breeding programs wishing to utilize GBS for the cost-effective genome-wide characterization of plant genetic resources, mainly in the absence of a reference genome. The pipeline, however, can also be used when a reference genome is available.

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