Abstract
SummaryGBS-SNP-CROP is a bioinformatics pipeline originally developed to support the cost-effective genome-wide characterization of plant genetic resources through paired-end genotyping-by-sequencing (GBS), particularly in the absence of a reference genome. Since its 2016 release, the pipeline’s functionality has greatly expanded, its computational efficiency has improved, and its applicability to a broad set of genomic studies for both plants and animals has been demonstrated. This note details the suite of improvements to date, as realized in GBS-SNP-CROP v.4.0, with specific attention paid to a new integrated metric that facilitates reliable variant identification despite the complications of homologs. Using the new de novo GBS read simulator GBS-Pacecar, also introduced in this note, results show an improvement in overall pipeline accuracy from 66% (v.1.0) to 84% (v.4.0), with a time saving of ∼70%. Both GBS-SNP-CROP versions significantly outperform TASSEL-UNEAK; and v.4.0 resolves the issue of non-overlapping variant calls observed between UNEAK and v.1.0.Availability and implementationGBS-SNP-CROP source code and user manual are available at https://github.com/halelab/GBS-SNP-CROP. The GBS read simulator GBS-Pacecar is available at https://github.com/halelab/GBS-Pacecar.Supplementary information Supplementary data are available at Bioinformatics online.
Highlights
The GBS-SNP-Calling Reference Optional Pipeline (GBS-SNPCROP) is an open-source pipeline that integrates custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving users full readable access to all intermediate files
Designed for paired-end reads, GBS-SNP-CROP employs a strategy of variant calling based on both within-individual and across-population patterns of polymorphism to identify and distinguish high-confidence variants from both sequencing and PCR errors, whether or not a reference genome is available
As a reference-optional pipeline, GBS-SNP-CROP has proven useful to breeders of under-researched crop species for which the lack of a reference genome presented a barrier to the efficient use of GBS data (Cheng et al, 2017; Hale et al, 2018; Melo et al, 2017; Sogbohossou et al, 2018; Wang et al, 2017)
Summary
The GBS-SNP-Calling Reference Optional Pipeline (GBS-SNPCROP) is an open-source pipeline that integrates custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving users full readable access to all intermediate files. Designed for paired-end reads, GBS-SNP-CROP employs a strategy of variant calling based on both within-individual and across-population patterns of polymorphism to identify and distinguish high-confidence variants from both sequencing and PCR errors, whether or not a reference genome is available. In the latter case, the pipeline uses a read-clustering strategy to build a so-called Mock Reference (MR) of consensus GBS fragments for use in downstream alignment, variant calling, and genotyping (Melo et al, 2016). DNumber of variants called by a pipeline (Note: a total of 35 000 variants were simulated, consisting of 25 000 SNPs and 10 000 indels).
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