<![CDATA[BOL: RGFA: powerful and convenient handling of assembly graphs]]> https://bioinformaticsonline.com/bookmarks/view/35345/rgfa-powerful-and-convenient-handling-of-assembly-graphs? https://bioinformaticsonline.com/bookmarks/view/35345/rgfa-powerful-and-convenient-handling-of-assembly-graphs Thu, 25 Jan 2018 05:47:53 -0600 https://bioinformaticsonline.com/bookmarks/view/35345/rgfa-powerful-and-convenient-handling-of-assembly-graphs <![CDATA[RGFA: powerful and convenient handling of assembly graphs]]> 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.

https://github.com/ggonnella/rgfa

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103826/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/35345/rgfa-powerful-and-convenient-handling-of-assembly-graphs#item-annotation-3715 Mon, 20 Jan 2020 05:39:22 -0600 https://bioinformaticsonline.com/bookmarks/view/35345/rgfa-powerful-and-convenient-handling-of-assembly-graphs#item-annotation-3715 <![CDATA[Comment by Rahul Nayak]]> The Graphical Fragment Assembly (GFA) is a proposed format which allow to describe the product of sequence assembly. This gem implements the proposed specifications for the GFA format described under https://github.com/GFA-spec/GFA-spec/blob/master/GFA-spec.md as close as possible.

]]> Rahul Nayak