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Wishlist

Overall requirements:

  • Complete analysis pipeline in Python, rather than partially/fully in MATLAB
  • Support for a free translocation workflow

Features to be implemented based on meeting, by processing step. Particular stakeholders are mentioned.

Input/Output

Tools for saving and reading sequencing files.

  • Extremely fast I/O

Preview tools

Methods for viewing measurement sessions for initial quality control.

  • ONT: Preliminary reports of channels, such as number of channels with good reads in the flow cell, along with duration of measurements
  • ONT: Information from multiplexer scans
  • ONT: Overview showing of measurements across all channels
  • Measurement information
  • ONT: Show flow-cell ID

Event detection/selection

Tools for detecting events/reads in measurements, in addition to filtering them by properties or by hand.

  • Event detection for short and plentiful events in free translocation (Tor, Luning)
  • GUI where even properties, e.g. dwell time or current drop/blockade are shown. Points in this plot can be selected can be selected, e.g. with a lasso to view/select a group of events and optionally create a consensus sequence.

Step finding

Tools to segment steps in events.

  • Step finding in short events (Tor)
  • Step finding for irregular steps (Tor)

Viewing and annotating events

Tools that allow for annotating (sections of) events.

  • Plotting power spectrum of a manually selected region in a raw trace (Luning)
  • Add a digital filter (4th-order Bessel filter) low-pass filter.
  • Allow for cleaning up and event by cutting parts, e.g. removing parts where the voltage is flipped/the pore is gating (Luning)
  • Option to assign a quality score to an event
  • Filtering events based on a certain pattern. Search for events that match a DNA/peptide sequence (Justas)
  • Manual inspection of events
  • Automatic selection of good events based on parameters for helicase sequencing/free translocation
  • Fast event loading, possibly by downsampling (Justas)
  • Splitting events/modifying the end of it, e.g for when two events follow each other rapidly and are segmented as one event
  • User-friendly method to segment and annotate multiple regions in events, i.e. DNA-peptide-reread-reread2.
  • Good live zoom feature.

Alignment/consensus generation

Methods for aligning two or more sequences including the creation of consensus sequences.

  • [] Alignment/consensus sequence generation
  • [] Tool to overlay two consensus sequences for comparison
  • [] Consensus generation for irregular steps (Tor)

Variant calling

Tools that allow for classification of events.

  • Variant calling module in Python

Potential resources

  • Ritmejeris, J., et al. (2025). "Terminal conjugation enables nanopore sequencing of peptides." bioRxiv: 2025.2011. 2012.687956.
  • Rukes, V., et al. (2025). "Charge-based fingerprinting of unlabeled full-length proteins using an aerolysin nanopore." bioRxiv: 2025.2001. 2013.632743.
  • Martin, A., et al. (2025). "Identification of Capture Phases in Nanopore Protein Sequencing Data Using a Deep Learning Model." arXiv preprint arXiv:2511.01277.
  • Plesa, C. and C. Dekker (2015). "Data analysis methods for solid-state nanopores." Nanotechnology 26(8): 084003.
  • Existing software from ONT/Elements/Axon instruments/Clampfit