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Updated: Jun 28, 2025

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

Fast and accurate variant identification tool for sequencing-based studies.

Jeffry M Gaston¹, Eric J Alm^2,3, An-Ni Zhang⁴

¹Google, Cambridge, USA.

|April 21, 2024

Summary

This summary is machine-generated.

QuickVariants is a new bioinformatics tool that identifies genetic variants faster and more accurately than bcftools. It excels in microbial studies, improving the detection of point mutations and insertions/deletions (indels).

Keywords:

Bioinformatics Genetic variants Microbiome SARS-CoV-2 Variant identification

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Last Updated: Jun 28, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Comparative Lesions Analysis Through a Targeted Sequencing Approach

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Published on: November 5, 2019

Area of Science:

Bioinformatics
Genomics
Microbial studies

Background:

Accurate identification of genetic variants (point mutations, indels) is vital for epidemic tracking, population genetics, and disease diagnosis.
Microbiome research necessitates high-speed, accurate, and robust variant identification tools for processing numerous sequencing datasets.

Purpose of the Study:

To introduce QuickVariants, a novel bioinformatics tool for summarizing variant information and identifying genetic variants.
To evaluate the speed and accuracy of QuickVariants compared to existing tools like bcftools, particularly for microbial sequencing data.

Main Methods:

Development of the QuickVariants bioinformatics tool for processing read alignments and identifying genetic variants.
Comparative analysis of QuickVariants against bcftools using diverse bacterial and viral (including SARS-CoV-2) sequencing data.
Assessment of variant identification accuracy, focusing on point mutations and indels, including analysis of specific variants like Omicron.

Main Results:

QuickVariants demonstrated a ninefold higher median speed than bcftools in bacterial sequencing data.
QuickVariants exhibited higher accuracy in identifying both point mutations and indels, with significantly fewer false negative indels for viral samples.
In sewage metagenomes, QuickVariants identified more Omicron-specific indels (5 vs. 0) and point mutations (61 vs. 48-54) than bcftools, which showed misinterpretation of indels.

Conclusions:

QuickVariants is a fast, accurate, and robust bioinformatics tool specifically designed for identifying genetic variants in microbial studies.
The tool offers improved performance over established methods like bcftools, particularly in handling indels.
QuickVariants is publicly available for use in genetic research.