Supporting data for "PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting"

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 pre-selection of informative variant sites with a population allele frequency around 0.5, which may be insufficient or unavailable for non-model organisms. As research expands to encompass a growing number of new species, a robust quality control tool will become increasingly important. <br>We developed PISAD, a tool for validating sample identities in whole-genome sequencing (WGS) data without requiring reference information. It uses a two stage approach: first, it performs rapid, reference-free SNP calling on low-error-rate data from the target individual to create a variant sketch; then, it assesses the concordance of other samples on this sketch to verify relationships. We assessed the performance and efficiency of PISAD on <i>Homo sapiens</i>, <i>Bos taurus</i>, <i>Gallus gallus</i>, <i>Arctia plantaginis</i> and <i>Pyrus</i> species. <br>Our evaluation showed that PISAD achieves a lower data coverage requirement (0.5×) compared to the reference-based tool ntsm and is broadly applicable to multiple diploid species.