Source 1primary paper2026MED
Toolkit/NGSTroubleFinder
NGSTroubleFinder
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
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.
Usefulness & Problems
No literature-backed usefulness or problem-fit explainer has been materialized for this record yet.
Published Workflows
Objective: Provide an integrated quality-control workflow for human NGS data that detects contamination, sample identity problems, kinship relationships, and sex mismatches from aligned sequencing files.
Why it works: The abstract states that the tool combines multiple analyses, including kinship, sex prediction, and contamination metrics, into a single report, allowing several data-integrity checks to be assessed together from the same aligned-input files.
cross-sample contamination detectionsample swap detectioninference of genetic and transcriptomic sexkinship inferencedirect BAM/CRAM analysisintegrated multi-analysis reporting
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
genetic and transcriptomic sex inferencekinship inferencesample identity concordance checkingsequence-based contamination detectionTarget processes
No target processes tagged yet.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
NGSTroubleFinder is written in Python, incorporates a custom parallelized pileup engine written in C, and is available through pip and containerized distribution.
NGSTroubleFinder can run directly on BAM or CRAM files without requiring an additional variant-calling step.
NGSTroubleFinder detects cross-sample contamination, sample swaps, and mismatches between reported and inferred genetic and transcriptomic sex in human whole-genome and whole-transcriptome sequencing data.
NGSTroubleFinder offers an integrated pipeline for NGS quality control that combines kinship, sex prediction, and contamination analyses into a detailed report.
Approval Evidence
1 source4 linked approval claimsfirst-pass slug ngstroublefinder
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.
Source:
implementationsupports
NGSTroubleFinder is written in Python, incorporates a custom parallelized pileup engine written in C, and is available through pip and containerized distribution.
Source:
input requirementsupports
NGSTroubleFinder can run directly on BAM or CRAM files without requiring an additional variant-calling step.
Source:
tool capabilitysupports
NGSTroubleFinder detects cross-sample contamination, sample swaps, and mismatches between reported and inferred genetic and transcriptomic sex in human whole-genome and whole-transcriptome sequencing data.
Source:
workflow integrationsupports
NGSTroubleFinder offers an integrated pipeline for NGS quality control that combines kinship, sex prediction, and contamination analyses into a detailed report.
Source:
Comparisons
No literature-backed comparison notes have been materialized for this record yet.
Ranked Citations
- 1.