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Updated: Mar 26, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis.

Nicholas A Tinker¹, Wubishet A Bekele², Jiro Hattori²

¹Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada nick.tinker@canada.ca.

G3 (Bethesda, Md.)

|January 29, 2016

Summary

This summary is machine-generated.

Haplotag is novel genotyping-by-sequencing (GBS) software that simplifies SNP discovery and haplotype-based genotyping. It operates without a reference genome, making GBS accessible for polyploid species and molecular breeding.

Keywords:

genotyping-by-sequencing (GBS)haplotype pipeline polyploidy single nucleotide polymorphism (SNP)

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Area of Science:

Genomics
Bioinformatics
Plant Breeding

Background:

Genotyping-by-sequencing (GBS) enables whole-genome genotyping for genomics, diversity analysis, and molecular breeding.
GBS data analysis is complex, requiring significant time, expertise, and computational resources.
Existing GBS methods often necessitate a reference genome, limiting their application in certain species.

Purpose of the Study:

To introduce Haplotag, a novel, user-friendly GBS software.
To enable efficient SNP discovery and haplotype-based genotyping without a reference genome.
To facilitate GBS applications in polyploid and self-pollinating plant species.

Main Methods:

Haplotag utilizes a tag-level haplotype model for polymorphism discovery within sequence tags.
The software operates in both discovery and production modes.
It does not require a reference genome and is optimized for polyploid species.

Main Results:

Haplotag successfully discovers single nucleotide polymorphisms (SNPs) and provides haplotype-based genotypes.
The software offers an intuitive visual "passport" for each inferred locus.
It requires minimal user investment and runs on widely available computer platforms.

Conclusions:

Haplotag offers a powerful, economical, and accessible GBS solution.
The software lowers the barrier to entry for GBS applications, particularly in non-model and polyploid organisms.
Haplotag supports advancements in plant genomics, diversity analysis, and molecular breeding.