Crate gfatk

gfatk is a tool for Graphical Fragment Assembly (GFA) manipulation.

GFA’s are at their heart, simple, directed graphs. As such, all internal representations of GFA’s are petgraph::Graph’s.

gfatk is designed mainly for reasonably small GFA files, and was designed for de-tangling and linearising plant mitochondrial genomes on the command line.

Almost all of the core functionality of gfatk resides in the gfatk::gfa module. The other modules are entry points for the command line application.

Modules

• dot
  Make a DOT language representation of a GFA.
• extract
  Extract a subgraph from a GFA.
• extract_chloro
  Extract the putative plastid subgraph in a GFA.
• extract_mito
  Extract the putative mitochondrial subgraph in a GFA.
• fasta
  Print all the sequences in a GFA to fasta format.
• gfa
  A module with all the methods to manipulate GFA’s in.
• linear
  Coerce a GFA into a fasta, finding the longest path through the graph.
• load
  Helper functions to load a GFA from a file, or read from STDIN. Modified from https://github.com/chfi/rs-gfa-utils/blob/2065b001d107ee9f5d7abe04d65ab82193fc5904/src/commands.rs
• overlap
  Generate overlapping sequences between segments in a GFA.
• path
  Extract a fasta given a path.
• rename
  Rename a GFA’s segment ID’s to a 1-indexed usize.
• stats
  Generate statistics about the input GFA file.
• trim
  Utility to trim a GFA of isolated nodes.
• utils
  Utility functions used throughout.