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Report utilities

Snippy-NG provides HTML report generation commands under snippy-ng utils report:

  • tree: render an interactive phylogenetic tree report from a Newick tree
  • sample: render an interactive per-sample variant report from a VCF

Commands

Command Purpose
Tree report Render an interactive phylogenetic tree report.
Sample report Render an interactive sample variant report.

Typical workflow

Generate a tree report after a multi-sample run:

snippy-ng utils gather --json --ref tests/data/reference.gbk tests/data/{wildtype,mutant}* > samples.json
snippy-ng multi samples.json --cpus 6 -o multi
snippy-ng tree --fast multi/core/core.095.aln -o multi/tree
snippy-ng utils report tree multi/tree/tree.treefile --metadata multi/snippy.vcf.summary.tsv -o multi/report

Generate a sample report from an existing VCF:

snippy-ng utils report sample short/snippy.pass.vcf -o short/report

See the dedicated pages for examples, screenshots, and command references.