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Updated: Jul 27, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting.

Zhantian Xu1,2,3, Fan Nie4, Jianxin Wang1,2,3,5

  • 1School of Computer Science and Engineering, Central South University, Changsha 410083, China.

Gigascience
|June 17, 2025
PubMed
Summary

Sample swaps in genomic sequencing are a major concern. PISAD (Phased Intraspecies Sample Anomalies Detection) is a new tool that validates sample identities in whole-genome sequencing data without needing reference information, making it broadly applicable.

Keywords:
k-mer analysisSNP callingquality controlreference-freesample swap

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic sequencing involves analyzing diverse data types, risking sample mislabeling.
  • Current methods need population references, which are unavailable for many species.
  • A robust quality control tool is crucial for expanding genomic research to new species.

Purpose of the Study:

  • To develop a reference-free tool for validating sample identities in whole-genome sequencing data.
  • To address the limitations of existing methods for nonmodel organisms.
  • To improve the accuracy and reliability of genomic data analysis.

Main Methods:

  • Developed PISAD (Phased Intraspecies Sample Anomalies Detection), a novel two-stage approach.
  • Stage 1: Reference-free single nucleotide polymorphism (SNP) calling to create a variant sketch from low-error data.
  • Stage 2: Assessing sample concordance against the variant sketch to verify relationships.

Main Results:

  • PISAD effectively validates sample identities across multiple species, including Homo sapiens, Bos taurus, Gallus gallus, Arctia plantaginis, and Pyrus species.
  • The tool requires significantly lower data coverage (0.5×) compared to reference-based methods.
  • Demonstrated broad applicability to various diploid species.

Conclusions:

  • PISAD provides a robust, reference-free solution for sample identity validation in whole-genome sequencing.
  • The tool overcomes limitations of existing methods, particularly for nonmodel organisms.
  • PISAD enhances the reliability of genomic research by minimizing sample swap errors.