ngs-quality-control

Standardize Illumina short-read sequencing quality control by orchestrating FastQC, fastp, samtools, and Picard to validate raw reads, trimmed data, and aligned BAM files. This pipeline supports WGS, WES, and targeted panels to ensure data integrity from raw FASTQ to aligned BAM.

Yes, you can generate a consolidated HTML quality report for WGS and WES samples. The pipeline aggregates metrics from FastQC, fastp, and samtools, flagging samples based on configurable quality thresholds to assess coverage and data standards.

Automate the sequencing QC lifecycle by running a multi-stage pipeline that validates raw reads, performs adapter trimming with fastp, and calculates alignment-based metrics via samtools and Picard. This ensures reproducibility from raw FASTQ files to aligned BAM outputs.

Yes, you need a Python environment with standard scientific libraries to aggregate samtools and Picard metrics. The qc_report.py script uses this environment to process FastQC outputs and flagstat files, producing a consolidated HTML quality report.

Assess WGS sample coverage standards before variant calling by generating an automated HTML summary report. The pipeline aggregates alignment-based metrics via samtools and Picard, flagging samples that fail configurable quality thresholds.

Yes, the pipeline supports targeted panel sequencing data alongside WGS and WES. It standardizes the quality control workflow by orchestrating FastQC, fastp, samtools, and Picard metrics to ensure data integrity from raw FASTQ to aligned BAM.