rgfa-simdebruijn
parse, edit and write GFA format graphs in Ruby
Install
- All systems
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curl cmd.cat/rgfa-simdebruijn.sh
- Debian
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apt-get install ruby-rgfa - Ubuntu
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apt-get install ruby-rgfa - Kali Linux
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apt-get install ruby-rgfa - Windows (WSL2)
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sudo apt-get updatesudo apt-get install ruby-rgfa - Raspbian
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apt-get install ruby-rgfa - Dockerfile
- dockerfile.run/rgfa-simdebruijn
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).