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MatchAlign  

Parsing GFA and GAF Alignment Files
View on CRAN: Click here


Download and install MatchAlign package within the R console
Install from CRAN:
install.packages("MatchAlign")

Install from Github:
library("remotes")
install_github("cran/MatchAlign")

Install by package version:
library("remotes")
install_version("MatchAlign", "0.1.2")



Attach the package and use:
library("MatchAlign")
Maintained by
Camille R. Mazurek
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-09-12
Latest Update: 2026-09-12
Description:
Provides tools for extracting segment paths from Graphical Fragment Assembly ('GFA') and Graph Alignment Format ('GAF') files. parse_paths_gfa() reads P (path) and W (walk) records and returns a named list of segment identifiers for each accession. parse_paths_gaf() parses the path string from each alignment and returns a named list of segments traversed by each query. parse_segment_lengths_gfa() reads S records and returns a named list of segment lengths keyed by segment identifier. These tools are intended to simplify downstream interpretation and analysis of pangenome graphs.
How to cite:
Camille R. Mazurek (2026). MatchAlign: Parsing GFA and GAF Alignment Files. R package version 0.1.2, https://cran.r-project.org/web/packages/MatchAlign. Accessed 24 Oct. 2026.
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