Expand description
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.