NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.

ABSTRACT: Quality control constitutes a critical component of any next-generation sequencing (NGS) pipeline; however, most existing pipelines emphasize technical quality assessment (e.g. read quality, alignment metrics, duplication rates) while overlooking other equally important dimensions, such as sample identity verification, contamination detection, kinship analysis, and metadata concordance. Detecting issues like cross-sample contamination and sample swaps is essential to control data integrity. Here, we present NGSTroubleFinder, a novel tool to detect cross-sample contamination in human whole-genome and whole-transcriptome sequencing data, sample swaps, and mismatches between the reported and the inferred genetic and transcriptomic sexes. It can be run directly on BAM/CRAM files without requir

SUBMITTER: Valentini S 

PROVIDER: S-EPMC12838523 | biostudies-literature | 2026 Mar

REPOSITORIES: biostudies-literature