RAMPART is a configurable pipeline for de novo assembly of DNA sequence data. RAMPART is not a de novo assembler. There are already many very good freely available assembly tools, however, few will produce a good assembly, suitable for annotation and downstream analysis, first time around. The reason for this is that genome assembly of non-model organisms are often complex and involve tuning of parameters and potentially, pre and post processing of the assembly. There are many combinations of tools that could be tried and no clear way of knowing a priori, which will work best.
RAMPART makes use of tried and tested tools for read pre-processing, assembly and assembly improvement, and allows the user to configure these tools and specify how they should be executed in a single configuration file. RAMPART also provides options for comparing and analysing sequence data and assemblies.
This functionality means that RAMPART can be used for at least 4 different purposes:
- Analysing sequencing data and understanding novel genomes.
- Comparing and testing different assemblers and related tools on known datasets.
- An automated pipeline for de novo assembly projects.
- Provides a single common interface for a number of different assembly tools.
The intention is that RAMPART gives the user the possibility of producing a decent assembly that is suitable for distribution and downstream analysis. Of course, in practice not every assembly project is so straight forward, the actual quality of assembly is always going to be a function of at least these sequencing variables:
- sequencing quality
- sequencing depth
- read length
- read insert size
... and the genome properties such as:
- genome size
- genome ploidy
- genome repetitiveness
RAMPART enables a bioinformatician to get a reasonable assembly, given the constraints just mentioned, with minimal effort. In many cases, particularly for organisms with haploid genomes or relatively simple (i.e. not too heterozygous and not too repeaty) diploid genomes, where appropriate sequenceing has been conducted, RAMPART can produce an assembly that suitable for annotation and downstream analysis.
RAMPART is designed with High Performance Computing (HPC) resources in mind. Currently, LSF and PBS schedulers are supported and RAMPART can execute jobs in parallel over many nodes if requested. Having said this RAMPART can be told to run all parts of the pipeline in sequence on a regular server provided enough memory is available for the job in question.
This documentation is designed to help end users install, configure and run RAMPART.
Comparison to other systems¶
Roll-your-own Make files This method probably offers the most flexibility. It allows you to define exactly how you want your tools to run in whatever order you wish. However, you will need to define all the inputs and outputs to each tool. And in some cases write scripts to manage interoperability between some otherwise incompatible tools. RAMPART takes all this complication away from the user as all input and output between each tool is managed automatically. In addition, RAMPART offers more support for HPC environments, making it easier to parallelize steps in the pipeline. Managing this manually is difficult and time consuming.
Galaxy This is a platform for chaining together tools in such a way as to promote reproducible analyses. It also has support for HPC environments. However, it is a heavy weight solution, and is not trivial to install and configure locally. RAMPART itself is lightweight in comparison, and ignoring dependencies, much easier to install. In addition, galaxy is not designed with de novo genome assembly specifically in mind, whereas RAMPART is. RAMPART places more constraints in the workflow design process as well as more checks initially before the workflow is started. In addition, as mentioned above RAMPART will automatically manage interoperability between tools, which will likely save the user time debugging workflows and writing their own scripts to manage specific tool interaction issues.
A5-miseq and BugBuilder Both are domain specific pipeline for automating assembly of microbial organisms. They are designed specifically with microbial genomes in mind and keep their interfaces simple and easy to use. RAMPART, while more complex to use, is far more configurable as a result. RAMPART also allows users to tackle eukaryote assembly projects.
iMetAMOS This is a configurable pipeline for isolate genome assembly and annotation. One distinct advantage of iMetAMOS is that it offers the ability to annotate your genome. It also supports some assemblers that RAMPART currently does not. Both systems are highly configurable, allowing the user to create bespoke pipelines and compare and validate the results of multiple assemblers. However, in it’s current form, iMetAMOS doesn’t have as much provision for automating or managing assembly scaffolding or gap filling steps in the assembly workflow. In addition, we would argue that RAMPART is more configurable, easier to use and has more support for HPC environments.