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escapepod

Alpha quality — under active development

escapepod is alpha software. APIs, CLI flags, and output formats may change without notice, and bugs are expected. Verify results against the official ONT pod5 tools before relying on it for anything important.

A fast, memory-efficient toolkit for reading and writing Oxford Nanopore POD5 files — available as a command-line tool, a Python package, and a Rust library, all backed by the same pure-Rust engine.

What is POD5?

POD5 is the native file format for Oxford Nanopore sequencing data. It stores:

  • Raw signal data — the electrical current measurements from the nanopore
  • Read metadata — information about each read (channel, timing, calibration)
  • Run information — experimental metadata (flow cell, protocol, sample)

Why escapepod?

  • Fast — memory-mapped I/O and efficient VBZ compression; up to ~9× faster than the official Python pod5 tools on large-file operations
  • Compatible — reads and writes files interchangeable with ONT tools, and the Python API mirrors the official pod5 package
  • One engine, three surfaces — the CLI, Python package, and Rust crates all share the same implementation
  • Safe — Rust's type system prevents whole classes of errors

Ways to use escapepod

Pick the surface that fits how you work:

I want to… Use Guide
Explore, filter, merge, and convert files from a shell the escpod CLI CLI Reference
Read/write POD5 in a Python script or notebook the escapepod package Python API
Embed POD5 I/O in a Rust program the escapepod-signal crate Rust Library
Understand or implement the on-disk format — File Format

Command line — escpod

# View reads in a POD5 file
escpod view experiment.pod5

# Merge multiple files, then filter by read ID
escpod merge -o combined.pod5 run1.pod5 run2.pod5
escpod filter -i interesting_reads.txt -o subset.pod5 combined.pod5

See the CLI Reference for every command.

Python — escapepod

A pod5-compatible package backed by the same Rust engine.

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import escapepod

with escapepod.Reader("experiment.pod5") as reader:
    print(f"{reader.read_count} reads")
    for read in reader:
        signal = reader.get_signal(read)   # numpy int16 (raw ADC)
        print(f"{read.read_id}: {read.num_samples} samples")

See the Python API for reading, writing, and signal helpers.

Rust

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use escapepod_signal::Reader;

let reader = Reader::open("experiment.pod5")?;

for read in reader.reads()? {
    let read = read?;
    println!("{}: {} samples", read.read_id, read.num_samples);

    // Get the raw signal
    let signal = reader.get_signal(&read.signal_rows)?;
}

See the Rust Library for the full crate API.

Getting Started

Documentation