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
• gfa
• handlegraph
• log
• quick-csv
• regex
• rustc-hash

Installation

From bioconda channel

Make sure you have conda installed!

conda install -c bioconda gfaffix

From binary release

Linux x86_64

wget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.1.5b/GFAffix-0.1.5b_linux_x86_64.tar.gz 
tar -xzvf GFAffix-0.1.5b_linux_x86_64.tar.gz 

# you are ready to go! 
./GFAffix-0.1.5b_linux_x86_64/gfaffix

MacOS X arm64

wget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.1.5b/GFAffix-0.1.5b_macos_x_arm64.tar.gz 
tar -xzvf GFAffix-0.1.5b_macos_x_arm64.tar.gz 

# you are ready to go! 
./GFAffix-0.1.5b_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

Command Line Interface

$ gfaffix --help
gfaffix 0.1.5b
Daniel Doerr <[email protected]>
Discover walk-preserving shared prefixes in multifurcations of a given graph.

    - Do you want log output? Call program with 'RUST_LOG=info gfaffix ...'
    - Log output not informative enough? Try 'RUST_LOG=debug gfaffix ...'

USAGE:
    gfaffix [OPTIONS] <GRAPH>

ARGS:
    <GRAPH>    graph in GFA1 format

OPTIONS:
    -c, --check_transformation
            Verifies that the transformed parts of the graphs spell out the identical sequence as in
            the original graph. Only for debugging purposes

    -h, --help
            Print help information

    -o, --output_refined <REFINED_GRAPH_OUT>
            Write refined graph in GFA1 format to supplied file [default: " "]

    -t, --output_transformation <TRANSFORMATION_OUT>
            Report original nodes and their corresponding walks in refined graph to supplied file
            [default: " "]

    -V, --version
            Print version information

    -x, --dont_collapse <NO_COLLAPSE_PATH>
            Do not collapse nodes on a given paths ("P" lines) that match given regular expression
            [default: " "]

Execution

RUST_LOG=info gfaffix examples/example1.gfa -o example1.gfa -t example1.trans > example1.shared_affixes