README.md

branchwater CLI client

Installation

Follow the instructions from the latest released version

Manual installation

Examples

From sequencing data

branchwater-client sequences.fa.gz > matches.csv 

From sequencing data, piping input

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

Using an existing sig

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

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

Available options

USAGE:
    branchwater-client [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