Quickstart Guide

Installation and configuration

With Bioconda

conda install segway

Generic installation

  1. To install Segway first install GMTK, and install HDF5, then run this command from bash:

    pip install segway
  2. If you are using SGE, your system administrator must set up a mem_requested resource for Segway to work. This can be done by installing Segway and then running python -m segway.cluster.sge_setup.

Acquiring data

  1. Observation data is stored with the genomedata system. <http://pmgenomics.ca/hoffmanlab/proj/genomedata/>. There is a small Genomedata archive for testing that comes with Segway, that is used in the below steps. You can get it using:

    wget http://pmgenomics.ca/hoffmanlab/proj/segway/2011/test.genomedata

Running Segway

  1. Use the segway train command to discover patterns in the test data. Here, we specify that we want Segway to discover four unique patterns:

    segway train --num-labels=4 test.genomedata traindir
  2. Use the segway identify command to create the segmentation, which partitions the genome into regions labeled with one of the four discovered patterns:

    segway identify test.genomedata traindir identifydir


This example spawns jobs that will run sequentially due to small segment size. See the --split-sequences option for dividing segments into smaller pieces.


  1. The identifydir/segway.bed.gz file has each segment as a separate line in the BED file, and can be used for further processing.

  2. The identifydir/segway.layered.bed.gz file is designed for easier visualization on a genome browser. It has thick lines where a segment is present and thin lines where it is not. This is not as easy for a computer to parse, but it is more useful visually.

  3. You can also perform further analysis of the segmentation and trained parameters using Segtools <http://pmgenomics.ca/hoffmanlab/proj/segtools/>.