curl -sSL skc.mbh.sh | sh
# or with wget
wget -nv -O - skc.mbh.sh | sh

$ curl -sSL skc.mbh.sh | sh -s -- --help
install.sh [option]

Fetch and install the latest version of skc, if skc is already
installed it will be updated to the latest version.

Options
        -V, --verbose
                Enable verbose output for the installer

        -f, -y, --force, --yes
                Skip the confirmation prompt during installation

        -p, --platform
                Override the platform identified by the installer

        -b, --bin-dir
                Override the bin installation directory [default: /usr/local/bin]

        -a, --arch
                Override the architecture identified by the installer [default: x86_64]

        -B, --base-url
                Override the base URL used for downloading releases [default: https://github.com/mbhall88/skc/releases]

        -h, --help
                Display this help message

cargo install skc

conda install skc

cargo build --release
./target/release/skc --help

$ skc -k 16 NC_001802.1.fa NC_000962.3.fa
[2023-06-20T01:46:36Z INFO ] 9079 unique k-mers in target
[2023-06-20T01:46:38Z INFO ] 2 shared k-mers between target and query
>4233642782 tcount=1 qcount=1 tpos=NC_001802.1:739 qpos=NC_000962.3:4008106
TGCAGAACATCCAGGG
>4237062597 tcount=1 qcount=1 tpos=NC_001802.1:8415 qpos=NC_000962.3:629482
CCAGCAGCAGATAGGG

$ skc --help
Shared k-mer content between two genomes

Usage: skc [OPTIONS] <TARGET> <QUERY>

Arguments:
  <TARGET>
          Target sequence

          Can be compressed with gzip, bzip2, xz, or zstd

  <QUERY>
          Query sequence

          Can be compressed with gzip, bzip2, xz, or zstd

Options:
  -k, --kmer <KMER>
          Size of k-mers (max. 32)

          [default: 21]

  -o, --output <OUTPUT>
          Output filepath(s); stdout if not present

  -O, --output-type <u|b|g|l|z>
          u: uncompressed; b: Bzip2; g: Gzip; l: Lzma; z: Zstd

          Output compression format is automatically guessed from the filename extension. This option is used to override that

          [default: u]

  -l, --compress-level <INT>
          Compression level to use if compressing output

          [default: 6]

  -h, --help
          Print help (see a summary with '-h')

  -V, --version
          Print version