Contiguity

Contig adjacency graph construction and visualisation.

Requirements

NCBI-BLAST+ >= 2.2.28 (needed for CAG creation, automatic self-comparisons and comparisons to a reference.
Bowtie-2 >= 2.1.0 (needed for CAG creation)
If you intend on creating graphs or generating comparisons from within Contiguity please ensure both are installed and in your path.

Manual

Contiguity Manual - PDF

Windows

Contiguity - Contiguity_1.0.4_win.zip
Khmer does not currently work on Windows, graphs are instead built using a Python dictionary, this may lead to performance issues. We recommend using OSX or Linux to build CAGs.

OSX

Contiguity - Contiguity_1.0.4_OSX_zip.

Linux

Contiguity - Contiguity_1.0.4_linux.tar.gz.

Python script

Contiguity - Contiguity.py.
Contiguity can also be run as a Python script - in addition to BLAST and Bowtie, this requires the Python library Khmer to be installed.

Example files

Example 1

CAG of E. coli str. UTI89 assembled from Illumina data. - example1.zip

Example 2

HGAP assembly of E. coli str. EC958 - Example coming soon.