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README.rst

Contiguity

Contiguity is a tool for constructing and visualising assembly graphs. It uses a linear layout so that the assembly graph can be directly compared to a reference.

Latest Version Downloads Build status

Contiguity Screen shot

Requirements:
  • Python 2.7+
  • NCBI-BLAST+ (needed for overlap edge creation and automatic comparison generation)
  • Bowtie 2 (needed for paired end edge creation)

Installation

If you're not familiar with the command-line we recommend you ask local IT support to help you install Contiguity.

Checking requirements are installed

You will need to install/have installed:
  • ncbiblast+ >= 2.2.28
  • python >= 2.7 (Python 3 is not supported)
  • bowtie2 >= 2.1.0

You can check these are installed by:

$ python --version
$ blastn -version
$ bowtie2 --version

Installation of python, blastn or bowtie2 (without a package manager) is beyond the scope of this document.

If you have both python, blastn and bowtie2 you need to (if not already present) install pip.

You can check if pip exists with:

$ which pip

If you get a "not found", please read the pip installation instructions.

If you already have pip we do suggest you upgrade it. We are using version 1.5.6 at the time of writing this document.

You can upgrade pip like this:

$ pip install --upgrade pip

pip based installation of Contiguity

If you have root/admin something like:

$ pip install Contiguity

Otherwise (not root/admin or permission denied errors running above):

$ pip install --user Contiguity

If you installed using the --user option of pip, Contiguity will typically end up in: /home/$USER/.local/bin/ You need to add this location to you ~/.bash_profile.

Add Contiguity to your path:

$ echo 'export PATH=$PATH:/home/$USER/.local/bin/' >> ~/.bash_profile
$ source !$

Testing the installation of Contiguity

Run (in the Terminal):

$ Contiguity

Upgrading Contiguity

You can upgrade like this:

pip install --upgrade Contiguity

Please regularly check back to make sure you're running the most recent Contiguity version.

Usage/Docs

For detailed information on how to use Contiguity please see the manual otherwise see Quick Start below.

Quick Start

Supported formats & the CAG

Contiguity works with ABySS (.dot), Velvet (LastGraph), Newbler (.ace) and SPAdes (FASTG) formats.

For all other assemblies, an assembly graph (.cag) can be created from the Contiguity GUI (file->create cag file) or using the command line.

We recommend that both Velvet and SPAdes graphs be reconstructed using the Contiguity CAG format.

You can read more about the CAG in the manual.

Generation of the CAG file

You can generate a CAG from the command line like:

$ Contiguity -cl -c <contig_file.fa> -fq <read_file.fq> -o <output_folder>
This assumes:
  • (~8GB of free memory)
  • contig_file.fa: is in FASTA file of contigs or scaffolds
  • read_file.fq: Interleaved fastq file - read1_left, read1_right, read2_left etc... orientated as such --> <--
  • output_folder: folder to put output files in, can and will overwrite files in this folder.

The resultant CAG file (output_folder/assembly.cag) can then be loaded into Contiguity.

The Contiguity GUI

There are 3 main functions of the Contiguity GUI -

Visualising an assembly graph:
  • Load FASTG/LastGraph/CAG etc. using "File->Load assembly"
  • View assembly graph using "View->View Assembly"
Compare assembly graph to a reference:
  • Load FASTG/LastGraph/CAG etc. using "File->Load assembly"
  • Create comparison to a reference by selecting "File->Create Comparison"
  • Select a reference file and click ok, when asked if you want to generate a comparison, click "yes".
  • View assembly graph using "View->View Assembly"
Self Comparison (Long read assemblies):
  • Load assembly (FASTA) using "File->Load assembly"
  • Create a self comparison using "View->Self Comparison"
  • Select "OK" and when asked if you want to generate a comparison, click "yes"

For more in depth description of functionality and work flows please see the manual.

Citation

If you use Contiguity in your work, please cite it using:

Mitchell J Sullivan, Nouri Ben Zakour, Brian Forde, Mitchell Stanton-Cook & Scott A Beatson*
Contiguity: Contig adjacency graph construction and visualisation
https://github.com/BeatsonLab-MicrobialGenomics/Contiguity
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