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.

The main website for contiguity can be found at http://mjsull.github.io/Contiguity

Contiguity can be downloaded from http://mjsull.github.io/Contiguity/files.html

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), GFA 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>

Or by selecting File > Create CAG in the GUI and providing a read file and a contig file

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:

Sullivan MJ, Ben Zakour NL, Forde BM, Stanton-Cook M, Beatson SA. (2015)
Contiguity: Contig adjacency graph construction and visualisation.
PeerJ PrePrints 3:e1273 https://dx.doi.org/10.7287/peerj.preprints.1037v1