DependenciesΒΆ

In order to do useful work RAMPART can call out to a number of third party tools during execution. The current list of dependencies is shown below. For full functionality, all these tools should be installed on your environment, however they are not mandatory so you only need to install those which you wish to use.

Assemblers (RAMPART is not an assembler itself so you should have at least one of these installed to do useful work):

  • Abyss V1.3
  • ALLPATHS-LG V44837
  • SOAPdenovo V2

Dataset improvement tools:

  • Sickle V1.1
  • Quake V0.3
  • Musket V1.0

Assembly improvement tools:

  • SSPACE Basic V2.0
  • SOAP GapCloser V1.12

Assembly Analysis Tools:

  • Quast V2.2 - for contiguity analysis
  • CEGMA V2.4 - for assembly completeness analysis
  • KAT V1.0 - for kmer analysis

Miscellaneous Tools:

  • TGAC Subsampler V1.0 - for reducing coverage of reads
  • Jellyfish V1.1.10 - for kmer counting

To save time finding all these tools on the internet RAMPART offers an option to download them all to a directory of your choice. The one exception to this is SSPACE, which requires you to fill out a form prior to download. To do this, after the core RAMPART pipeline is compiled, type: rampart-download-deps <dir>. Executing this command does not try to install the tools, as this is a complex process and you may wish to run a custom installation in order to compile and configure the tools in a way that is optimal for your particularly environment.

In case the specific tool versions requested are no longer available to download the project URLs are specified below. It’s possible alternative (preferably newer) versions of the software may still work if the interfaces have not changed significantly. If you find that a tool does not work in the RAMPART pipeline please contact daniel.mapleson@tgac.ac.uk, or raise a job ticket via the github issues page: https://github.com/TGAC/RAMPART/issues.

Project URLs: