gfadiff

parse, edit and write GFA format graphs in Ruby

Install

All systems
curl cmd.cat/gfadiff.sh
Debian Debian
apt-get install ruby-rgfa
Ubuntu
apt-get install ruby-rgfa
image/svg+xml Kali Linux
apt-get install ruby-rgfa
Windows (WSL2)
sudo apt-get update sudo apt-get install ruby-rgfa
Raspbian
apt-get install ruby-rgfa

ruby-rgfa

parse, edit and write GFA format graphs in Ruby

The Graphical Fragment Assembly (GFA) format is a proposed file format to describe the product of a genome sequence assembly process. rgfa implements the proposed specifications for the GFA format described under https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md as closely as possible. The library allows one to create an RGFA object from a file in the GFA format or from scratch, to enumerate the graph elements (segments, links, containments, paths and header lines), to traverse the graph (by traversing all links outgoing from or incoming to a segment), to search for elements (e.g. which links connect two segments) and to manipulate the graph (e.g. to eliminate a link or a segment or to duplicate a segment distributing the read counts evenly on the copies).