gene-extractor

A command line app to extract gene from genomic contigs. The program requires phyluce and its dependencies to run. Future update may interact directly with Lastz, BWA-MEM or both.

Installation

genx is a single executable command line app. The executable file will be available in the release link. Copy it to the folder that is registered in your PATH variable.

You can also install the app using the Rust package manager cargo:

cargo install genx

OS support:

1. MacOS
2. Linux
3. Windows-WSL

Dependencies:

Phyluce and its depedencies (install here).

Usages

Subcommand options:

USAGE:
    genx <SUBCOMMAND>

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

SUBCOMMANDS:
    check      Check dependencies
    extract    Batch gene tree estimation using IQ-Tree
    help       Prints this message or the help of the given subcommand(s)

Command options extract the gene:

USAGE:
    genx extract --dir <PATH> --output <PATH> --refs <PATH>

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -d, --dir <PATH>       Path to contig directory
    -o, --output <PATH>    Path to output files
    -r, --refs <PATH>      Path to reference fasta files