Introduction

The "Graphical Fragment Assembly" (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA can be employed to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g., to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs.

Publications

  1. RGFA: powerful and convenient handling of assembly graphs.
    Cite this
    Gonnella G, Kurtz S, 2016-01-01 - PeerJ

Credits

  1. Giorgio Gonnella
    Developer

    Zentrum für Bioinformatik, Universität Hamburg, Germany

  2. Stefan Kurtz
    Investigator

    Zentrum für Bioinformatik, Universität Hamburg, Germany

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Summary
AccessionBT006754
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByStefan Kurtz