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Launch the Ninetails Analysis Dashboard (Guppy Legacy)

Source: R/ninetails_app_launcher_guppy.R
launch_signal_browser_guppy.Rd

Opens an interactive Shiny application for exploring ninetails results from the Guppy legacy pipeline (check_tails_guppy). This is the fast5-based counterpart of launch_signal_browser, designed for data basecalled with Guppy \(\le\) 6.0.0 using Nanopolish poly(A) coordinates.

Usage

launch_signal_browser_guppy(
  config = NULL,
  nanopolish_file = NULL,
  sequencing_summary_file = NULL,
  workspace = NULL,
  class_file = NULL,
  residue_file = NULL,
  basecall_group = "Basecall_1D_000",
  ...
)

Arguments

config

Character string (optional). Path to a YAML configuration file defining multiple samples. When provided, single-sample arguments are ignored.

nanopolish_file

Character string (optional). Path to the Nanopolish polya output file. Required for the Signal Viewer tab in single-sample mode.

sequencing_summary_file

Character string (optional). Path to the Guppy sequencing summary file. Required for the Signal Viewer tab in single-sample mode.

workspace

Character string (optional). Path to the directory containing multi-fast5 files. Required for the Signal Viewer tab in single-sample mode.

class_file

Character string (optional). Path to the read_classes output file from check_tails_guppy().

residue_file

Character string (optional). Path to a nonadenosine_residues output file from ninetails.

basecall_group

Character string. Fast5 hierarchy level for basecall data extraction. Default: "Basecall_1D_000".

...

Additional arguments passed to runApp.

Value

Launches a Shiny application (does not return a value).

Details

The dashboard provides the same six tabs as the Dorado version (Classification, Residues, Poly(A) length, Signal Viewer, Download, About), with two Guppy-specific additions:

Nanopolish QC

Additional plot in the Classification tab showing the distribution of Nanopolish QC tags (PASS, ADAPTER, NOREGION, SUFFCLIP, etc.) via plot_nanopolish_qc().

Fast5 Signal Viewer

Uses plot_squiggle_fast5() and plot_tail_range_fast5() instead of POD5-based functions. Includes a moves toggle to show/hide basecaller move transitions. No Python dependency required.

The YAML configuration file should have the following structure:


samples:
  sample_label:
    sample_name: WT_rep1
    group: WT
    class_path: /path/to/read_classes.txt
    residue_path: /path/to/nonadenosine_residues.txt
    polya_path: /path/to/nanopolish_output.tsv         # optional
    seq_summary: /path/to/sequencing_summary.txt      # optional
    workspace: /path/to/fast5/                        # optional

See also

launch_signal_browser for the Dorado DRS version, check_tails_guppy for the Guppy pipeline.

Examples

if (FALSE) { # \dontrun{

# Multi-sample mode
ninetails::launch_signal_browser_guppy(config = "config_guppy.yml")

# Single-sample: all tabs
ninetails::launch_signal_browser_guppy(
  nanopolish_file = "/path/to/nanopolish_output.tsv",
  sequencing_summary_file = "/path/to/sequencing_summary.txt",
  workspace = "/path/to/fast5/",
  class_file = "/path/to/read_classes.txt",
  residue_file = "/path/to/nonadenosine_residues.txt"
)

} # }