poretools: a toolkit for working with nanopore sequencing data from Oxford Nanopore.

The MinION (TM) from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialised and is now available to early-access users. The MinION (TM) is a USB-connected, portable nanopore sequencer which permits real-time analysis of streaming event data. Currently, the research community lacks a standardized toolkit for the analysis of nanopore datasets.

We have therefore develped poretools, a flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Poretools operates directly on the native FAST5 (a variant of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools.

A preprint of the poretools manuscript is available on bioarxiv: http://biorxiv.org/content/early/2014/07/23/007401

Below are a few examples of common usage.

  1. Extract sequences in FASTQ format from a set of FAST5 files.
poretools fastq fast5/
  1. Make a collector’s curve of the yield from a sequencing run.
poretools yield_plot --plot-type reads fast5/
  1. Plot a histogram of read sizes from a set of FAST5 files.
poretools hist fast5/



Please note that Anaconda and Python(x,y) already have all these dependencies installed: Anaconda (Linux, Windows, OS X): https://store.continuum.io/cshop/anaconda/ Python(x,y) (Windows): https://code.google.com/p/pythonxy/