Interpreting results

The PDF report

The report is intended to be read quickly:

  • A summary of read filtering / subsampling

  • A view of haplotype clustering / OTUs

  • Optional BLAST tables (if enabled and available)

  • A haplotype distance matrix summary

If a figure is missing in the PDF, see FAQ / Troubleshooting (common causes: missing matplotlib/Pillow, or a plotting backend issue on headless systems).

FASTA outputs

Typical FASTA outputs include:

  • high-frequency haplotypes

  • low-frequency haplotypes

  • suspected chimeras

The exact filenames are documented in Outputs.

JSON report

The JSON report mirrors the PDF in machine-readable form:

  • run configuration (parameters)

  • read statistics

  • haplotype/cluster summaries

  • file paths for generated artifacts

This is useful if you want to post-process results in R/Python.