PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting.

ABSTRACT:

Background

Genomic sequencing research often requires the simultaneous analysis of heterogeneous data types across single or multiple individuals, introducing a substantial risk of sample swaps (e.g., labeling errors). Existing methods primarily rely on reference information, requiring the preselection of informative variant sites with a population allele frequency around 0.5, which may be insufficient or unavailable for nonmodel organisms. As research expands to encompass a growing number of new species, a robust quality control tool will become increasingly important.

Finds

We developed PISAD (Phased Intraspecies Sample Anomalies Detection), a tool for validating sample identities in whole-genome sequencing (WGS) data without requiring reference information. It uses a 2-st

SUBMITTER: Xu Z 

PROVIDER: S-EPMC12202988 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature