GFAffix

GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.

Dependencies

GFAffix is written in RUST and requires a working RUST build system for installation. See https://www.rust-lang.org/tools/install for more details.

It makes use of the following crates:

• clap
• env_logger
• flate2
• gfa
• handlegraph
• indexmap
• log
• rayon
• regex
• rustc-hash

Installation

From bioconda channel

Make sure you have conda/mamba installed!

mamba install -c conda-forge -c bioconda gfaffix

From binary release

Linux x86_64

wget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.2.0/GFAffix-0.2.0_linux_x86_64.tar.gz 
tar -xzvf GFAffix-0.2.0_linux_x86_64.tar.gz 

# you are ready to go! 
./GFAffix-0.2.0_linux_x86_64/gfaffix

MacOS X arm64

wget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.2.0/GFAffix-0.2.0_macos_x_arm64.tar.gz 
tar -xzvf GFAffix-0.2.0_macos_x_arm64.tar.gz 

# you are ready to go! 
./GFAffix-0.2.0_macos_x_arm64/gfaffix

From repository

# install GFAffix
git clone https://github.com/marschall-lab/GFAffix.git
# build program
cargo build --manifest-path GFAffix/Cargo.toml --release
# built binary is located at GFAffix/target/release/gfaffix

Command Line Interface

$ gfaffix --help
Discover and collapse walk-preserving shared affixes of a given variation graph.

Usage: gfaffix [OPTIONS] <GRAPH>

Arguments:
  <GRAPH>  graph in GFA1 format, supports compressed (.gz) input

Options:
  -o, --output_refined <REFINED_GRAPH_OUT>
          Write refined graph output (GFA1 format) to supplied file instead of stdout; if file name
          ends with .gz, output will be compressed [default: ]
  -t, --output_transformation <TRANSFORMATION_OUT>
          Report original nodes and their corresponding walks in refined graph to supplied file
          [default: ]
  -c, --check_transformation
          Verifies that the transformed parts of the graphs spell out the identical sequence as in the
          original graph
  -a, --output_affixes <AFFIXES_OUT>
          Report identified affixes [default: ]
  -x, --dont_collapse <NO_COLLAPSE_PATH>
          Do not collapse nodes on a given paths/walks ("P"/"W" lines) that match given regular
          expression [default: ]
  -p, --threads <THREADS>
          Run in parallel on N threads [default: 1]
  -v, --verbose
          Sets log level to debug
  -h, --help
          Print help
  -V, --version
          Print version

Execution

gfaffix -c examples/example1.gfa -o example1.gfa > example1.gfaffixed.gfa