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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. 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.
Facet | Computational Load | Link |
---|---|---|
General Metrics | Light | Click here |
Template Length Metrics | Light | Click here |
GC Content Metrics | Light | Click here |
Genomic Features Metrics | Moderate |
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Subcommands
ngs convert
ngs derive
ngs generate
ngs index
ngs list
ngs plot
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ngs qc
- Record-based Facets
- Sequence-based Facets
ngs view
- Development