ngs qc

The ngs qc subcommand provides tools for checking the quality of next-generation sequencing files. This subcommand is compromised of multiple quality check facets which are configurable for the level of QC you wish to generate. Each quality check facet has a dedicated page within the wiki to explore.

Each facet has an associated computational load. In this context, a computational load is a mostly-subjective determination regarding how much time a facet adds to the overall run (some facets greatly increase the runtime while others do not). In under normal operating conditions,

• Light computational loads increase the runtime by less than 1 second per million reads.
• Moderate computational loads increase the runtime by between 1 and 5 seconds per million reads.
• Heavy computational loads increase the runtime by more than 5 seconds per million reads.

The following quality check facets are currently supported.

Facet	Computational Load	Link
Summary Metrics	Light
Template Length Metrics	Light
GC Content Metrics	Light
Genomic Features Metrics	Moderate