Pod5 File Format Documentation

Date:

Jun 03, 2024

Version:

0.3.10

POD5 is a file format for storing nanopore sequencing data in an easily accessible way. The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format.

Data in POD5 is stored using Apache Arrow, allowing users to consume data in many languages using standard tools.

This project contains a core library for reading and writing POD5 data, and a toolkit for accessing this data in other languages.

Install

POD5 is also bundled as a python module for easy use in scripts, a user can install using:

To install the latest python release, type:

$ pip install pod5

This python module provides the python library to write custom scripts against. See the Installation Documentation for further details.

Contents

• Install
  • Install pod5
  • Installation from Source
  • Python Development Setup
• Getting Started
  • Reading POD5 Files
  • Writing POD5 Files
• Reading POD5 Datasets
  • Loading a Dataset
  • Iterate Over Reads
  • Random Access to Records
• Tools
  • pod5 view
  • pod5 inspect
  • pod5 merge
  • pod5 filter
  • pod5 subset
  • pod5 repack
  • pod5 convert fast5
  • pod5 convert to_fast5
  • pod5 update

Reference Documentation

• Python API Reference
• Python Tools Reference
• POD5 File Format Design Details
• POD5 Format Specification

Indices and Tables

• Index

• Module Index

• Search Page