Command line usage of nanalogue

Tutorials

The following tutorials demonstrate common workflows with nanalogue:

• Quick look at your data — Initial inspection of BAM files to see contigs and modification types
• Quality control of mod data — Assess modification call quality and apply filters
• Extract raw mod calls — Get raw modification data from BAM files
• Extracting sequences — Display read sequences with indel and modification highlighting
• Finding highly modified reads — Filter reads by modification level
• Exploring modification gradients — Detect directional patterns in modification data
• Region-specific analysis — Focus analysis on specific genomic regions
• Recipes — Quick copy-paste snippets for common tasks

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.