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TailfindR compatibility

Source: vignettes/tailfindr.Rmd
tailfindr.Rmd

Note: TailfindR compatibility applies only to the Guppy legacy pipeline (check_tails_guppy()).

Since version 1.0.2, ninetails is compatible with tailfindR.

We still recommend nanopolish polya for determining tail coordinates because:

  • The ninetails model was trained on Nanopolish output
  • Nanopolish provides quality metrics that ninetails uses for filtering
  • Nanopolish manages resources better and works faster

However, for users who prefer tailfindR, we provide compatibility functions.

Using ninetails with tailfindR output

Step 1: Convert tailfindR output

Before running the pipeline, convert tailfindR output to ninetails-compatible format:

converted_tailfindr <- ninetails::convert_tailfindr_output(
  tailfindr_output = '/path/to/tailfindr/output.csv'
)

Step 2: Run the pipeline

Pass the converted output to check_tails_guppy() as the polya_data argument:

results <- ninetails::check_tails_guppy(
  polya_data = converted_tailfindr,
  sequencing_summary = '/path/to/sequencing_summary.txt',
  workspace = '/path/to/workspace',
  num_cores = 2,
  basecall_group = 'Basecall_1D_000',
  pass_only = TRUE,
  save_dir = '~/output/'
)

Important caveats

No quality metrics

TailfindR does not provide signal quality metrics like Nanopolish does. This means:

  • Signals with poor quality may be included in the analysis
  • With Nanopolish, such signals would be filtered based on the quality tag
  • Results from tailfindR should be treated with additional caution

Not seamlessly integrated

Due to the quality metric limitation, ninetails has not been seamlessly integrated with tailfindR like it has with Nanopolish. The explicit conversion step is required.

Comparison

Feature Nanopolish TailfindR
Quality metrics ✅ Yes ❌ No
Resource management Better Variable
Speed Faster Variable
Ninetails integration Seamless Requires conversion
Recommendation Preferred Use with caution

Summary

For best results with the Guppy legacy pipeline:

  1. Preferred: Use nanopolish polya output directly
  2. Alternative: Convert tailfindR output using convert_tailfindr_output(), but interpret results cautiously

For new analyses, we recommend using the Dorado DRS pipeline (check_tails_dorado_DRS()) instead of the Guppy legacy pipeline.