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GFA: Graphical Fragment Assembly (GFA) Format Specification
We are developing the specification of the Graphical Fragment Assembly (GFA) format. Your contribution is welcome. Please open up issues or submit pull requests.
Examples of sequence overlap graphs (assembly graphs) in a variety of formats
GFA 2.0: Graphical Fragment Assembly (GFA2) Format Specification 2.0
Jason Chin, Richard Durbin, and myself (Gene Myers) found ourselves together at a workshop
meeting in Dagstuhl Germany and hammered out an initial proposal for an assembly format.
We started with GFA 1 and proceeded to build a
more comprehensive design around it. After extensive revision and discussion on Github with
the GFA group including Shaun Jackman, Heng Li, and Giorgio Gonnella, we arrived at
GFA 2.0. The standard is an evolving effort, and your contribution is welcome. Please open up issues or submit pull requests.
The basic reason for having a standard format is that we find that
in general, different development teams build assemblers, visualizers, and editors because
of the complexity and distinct nature of the three tasks. While these tools should certainly
use tailored encodings internally for efficiency, the nexus between the three efforts
benefits from a standard encoding format that would make them all interoperable.
GFA 1.0
GFA 1 was first suggested in a blog post by Heng Li (@lh3) and further developed in a second post.
GFA 1.1
W-lines were suggeseted by Heng Li (@lh3) as an extension to GFA 1 for representing haplotype information in pangenome graphs.
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Graphical Fragment Assembly (GFA) Format Specification
