Requirements

Viewing assembly graphs

Contiguity comes as a compiled package for Windows, OSX and GNU/Linux. If you would like Contiguity to automatically generate comparison files for you, please have BLAST installed and in your path. Contiguity also accepts user generated comparison files in BLAST's tabbed output format with no headers (-outfmt 6).

Running as a Python script

Python – Contiguity has been tested using python 2.7, use earlier versions at your own risk.

Tkinter (GUI) – Included in most installations of Python.

Constructing contig adjacency graphs with Contiguity

NCBI-BLAST+ – BLAST is required for generating CAG files. Available at http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download.

Bowtie 2 – Bowtie 2 is required for generating CAG files with paired-end data. Available at http://bowtie-bio.sourceforge.net/bowtie2/index.shtml/.

Khmer – While not required, it is strongly recommended you use Khmer to generate the CAG file unless you have a large amount of memory (>=16GB) a smallish sequencing run (<6Mbp genome with < 200x coverage) and a lot of time. Khmer comes packaged with the Linux and OSX versions of Contiguity and does not require installation. Khmer is Available at https://github.com/ged-lab/khmer.

Not all versions of Khmer are supported, please check REQUIREMENTS.txt on the github page for required version.