analysis

Quality Analysis

Quality scoring, contamination detection, and outlier analysis for sequencing data (FASTQ, VCF, BAM).

Contents

File	Purpose
contamination.py	Contamination detection: RNA, vector, adapter, cross-species, mycoplasma
metrics.py	Quality scoring, outlier detection, integrity checks, batch analysis

Key Classes and Functions

Symbol	Description
ContaminationDetector	Class for multi-type contamination screening
detect_rna_contamination()	Check DNA sequences for RNA contamination
detect_vector_contamination()	Screen for vector backbone sequences
detect_adapter_contamination()	Identify adapter sequence remnants
generate_contamination_report()	Full contamination screening report
calculate_quality_score()	Composite quality score for FASTQ, VCF, or BAM
detect_outliers()	Statistical outlier detection (IQR or z-score)
calculate_data_integrity_score()	Data completeness and consistency score
generate_quality_report()	Multi-section quality assessment report
batch_quality_analysis()	Run quality analysis across multiple samples

Usage

from metainformant.quality.analysis.metrics import calculate_quality_score, detect_outliers
from metainformant.quality.analysis.contamination import ContaminationDetector

score = calculate_quality_score(fastq_data, data_type="fastq")
outliers = detect_outliers(quality_values, method="iqr")
detector = ContaminationDetector(sequences)