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Utilities

Snippy-NG provides utility commands that support the main SNP-calling pipelines.

Reference utilities

  • ref: prepare a reference genome for Snippy-NG
  • gather: discover sample files and write input for snippy-ng multi

Alignment utilities

  • samclip: filter clipped reads from SAM alignments using a boundary-aware terminal clipping rule
  • cnv: estimate contig or feature copy numbers from aligned BAM or CRAM depth

Report generation

  • tree: render an interactive phylogenetic tree report
  • sample: render an interactive per-sample variant report

See the individual command pages for usage examples and option details.