What are the main quality-control checkpoints in an NGS workflow?

Why

I would structure QC around the decisions each stage enables. Before sequencing, confirm chain of custody, nucleic acid integrity and quantity, and suitable library insert size or enrichment. After the run, review yield, per-cycle base quality, adapter content, read-length distribution and run controls.

Following alignment, examine mapping rates, insert sizes, duplication, coverage uniformity and low-quality or uncovered regions. For a variant assay, include informative depth, allele balance, strand support, reference-specific biases and sample-identity checks. Thresholds are application dependent.

A germline exome, tumor panel and RNA-seq experiment need different acceptance criteria. For example, a sample can pass global Q30 expectations but have insufficient coverage of a clinically important exon. Define validated thresholds and investigate failures as potential preparation, run or analysis issues before release.

A QC pass is evidence of fitness for a specified purpose, not a guarantee that every biological conclusion is correct.