Command line usage of nanalogue
For detailed documentation of all CLI commands and options, see the CLI Commands Reference.
The CLI Commands Reference is automatically generated from the latest version of the nanalogue package and provides comprehensive help text for all commands and subcommands.
Common options
Most if not all CLI commands have options to filter by:
- minimum sequence or alignment length
- alignment quality
- alignment type (primary/secondary/supplementary/unmapped)
- read ids
- mod quality
- base quality
You can also perform subsampling, trim by read ends etc. Please see the CLI commands reference shown above.