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Getting the software

To run this tutorial you will need some software. This page will get you set up.

You need a version of the following tools:

  • samtools, a program for manipulating next-generation sequencing data reads
  • fastqc, a program for performing quality control fo sequence data
  • bwa, a program for aligning reads to a reference sequence
  • jellyfish 2, a program for counting k-mers (short sequences of fixed length k) in sequence data reads.
  • And it is also useful to install the Integrated Genomics Viewer.

You can get this software in a few different ways:

  • If you are working on a JupyterHub instance we have setup, these tools should be installed already.
  • If you have set up a conda installation as described here (including the bioconda and conda-forge channels), you should be able to install everything except IGV with the command
conda install samtools fastqc bwa jellyfish

or if mamba isn't working,

mamba install samtools fastqc bwa jellyfish

run in your UNIX terminal.

The IGV desktop application has to be downloaded and installed seperately - see the IGV website.

If neither of these work, you may be able to install using your system's package manager (such as apt on Ubuntu) or by building from source. Doing this is out of scope of this tutorial but if you know what you're doing, feel free to try this.

Testing it. To check that you have the right software, open a bash terminal and try getting them to print their version information. You should see something like:

$ jellyfish --version
jellyfish 2.3.0

$ fastqc --version
FastQC v0.11.9

$ samtools --version
samtools 1.8
Using htslib 1.8
Copyright (C) 2018 Genome Research Ltd.

$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

[...]

(Don't type the dollar signs, those are just there to indicate the command prompt.)

When you've got the software get the data.