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.

Facet	Computational Load	Facet Type	Link
General Metrics	Light	Record-based	Click here
GC Content Metrics	Light	Record-based	Click here
Template Length Metrics	Light	Record-based	Click here
Genomic Features Metrics	Moderate	Record-based	Click here
Quality Score Metrics	Moderate	Record-based	Click here
Coverage Metrics	Moderate	Sequence-based	Click here
Edit Metrics	Heavy	Sequence-based	Click here

Computational load

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. We provide this classification so one can easily determine which QC facets are feasible to run on their infrastructure.

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

The following quality check facets are currently supported.