README.md

branchwater CLI client

Installation

MacOS (Apple Silicon)

curl -o branchwater -L https://github.com/sourmash-bio/branchwater/releases/latest/download/branchwater-client-aarch64-apple-darwin
chmod +x branchwater

MacOS (Intel)

curl -o branchwater -L https://github.com/sourmash-bio/branchwater/releases/latest/download/branchwater-client-x86_64-apple-darwin
chmod +x branchwater

Linux (arm)

curl -o branchwater -L https://github.com/sourmash-bio/branchwater/releases/latest/download/branchwater-client-arm-unknown-linux-gnueabihf
chmod +x branchwater

Linux (x86_64)

curl -o branchwater -L https://github.com/sourmash-bio/branchwater/releases/latest/download/branchwater-client-x86_64-unknown-linux-musl
chmod +x branchwater

Windows (x86_64)

Invoke-WebRequest -Uri 'https://github.com/sourmash-bio/branchwater/releases/latest/download/branchwater-client-x86_64-pc-windows-msvc.exe' -OutFile branchwater

Examples

From sequencing data

./branchwater sequences.fa.gz > matches.csv 

From sequencing data, piping input

cat sequences.fa | ./branchwater -o matches.csv -

Using an existing sig

Note: sig needs to be built using k=21, scaled=1000

./branchwater --sig -o matches.csv \
  <(curl -sL https://wort.sourmash.bio/v1/view/genomes/GCF_000195915.1)

Available options

USAGE:
    branchwater [OPTIONS] <SEQUENCES>

ARGS:
    <SEQUENCES>    Input file. Can be:
                     - sequences (FASTA/Q, compressed or not)
                     - an existing signature (use with --sig)
                     - a single dash ("-") for reading from stdin

OPTIONS:
    -h, --help               Print help information
    -o, --output <OUTPUT>    Save results to this file. Default: stdout
        --sig                Input file is already a signature
    -V, --version            Print version information