NGS Quality Control

Overview

This skill encodes a reproducible QC workflow for Illumina short-read sequencing data across the full lifecycle: raw reads → trimmed reads → aligned BAMs. It produces deterministic metrics suitable for QC gating in WGS, WES, and targeted panel projects.

Pipeline stages:

1. Raw-read QC — FastQC per FASTQ, aggregated with MultiQC.
2. Adapter/quality trimming — fastp with paired-end adapter detection.
3. Post-trim QC — FastQC + MultiQC on trimmed reads.
4. Alignment QC — samtools stats/flagstat, Picard metric suites.
5. Coverage QC — mosdepth (genome windows or target BED).
6. Aggregation — MultiQC over all tool outputs for a single-HTML summary.

Usage

Assume THREADS=8, OUT=qc_out, paired FASTQs sample_R1.fastq.gz / sample_R2.fastq.gz, coordinate-sorted sample.bam with index, reference ref.fasta, and (for WES/panel) target intervals.