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A pipeline for creating multiple assemblies and a framework for analysing and comparing them. Rampart supports a variety of third-party tools for assembling, scaffolding and read error correction. After assembling contigs using different tools and parameters, it produces statistics and plots enabling the user to interpret, compare and visualise results. Rampart uses metrics based on this information to assign scores to each assembly, highlighting which set of assembled contigs should be considered for further scaffolding and enhancement. This methodology enables rampart to evaluate its final assembly in the absence of a reference.

Software type:
Framework, Pipeline
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
Java
License:
GNU General Public License version 2.0
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Daniel Mapleson <daniel.mapleson at tgac.ac.uk>

Institution(s)

The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK

  • (Mapleson et al., 2015) RAMPART: a workflow management system for de novo genome assembly. Bioinformatics.
    PMID: 25637556
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    PMID: 21559467
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    PMID: 22676195
  • (Kleftogiannis et al., 2013) Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PloS one.
    PMID: 24086547
  • (Nagarajan and Pop, 2013) Sequence assembly demystified. Nature reviews Genetics.
    PMID: 23358380
  • (Bradnam et al., 2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience.
    PMID: 23870653
  • (Salzberg et al., 2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome research.
    PMID: 22147368
  • (Utturkar et al., 2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics.
    PMID: 24930142
  • (Alkan et al., 2011) Limitations of next-generation genome sequence assembly. Nature methods.
    PMID: 21102452
  • (Love et al., 2016) Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC genomics.
    PMID: 26944054

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