sourmash-mixers

sourmash-mixers is a meta-package to install a number of useful sourmash plugins!

Our intention is that all "suitably mature" sourmash plugins will be available via sourmash-mixers, at least for now. "Maturity" rubrics are defined here, but it's an evolving criteria...

The list of plugins installed by sourmash-mixers is available in pyproject.toml under dependencies - the list includes:

• a command-line plugin to produce 2- and 3-way Venn diagrams of sketches
• a command-line plugin to sketch many samples or genomes
• a command-line plugin to download NCBI genomes by accession
• a command-line plugin to filter hashes by presence/absence in multiple samples
• a command-line plugin to plot abundance histograms

Installation

This command:

pip install sourmash-mixers

will install the latest version of sourmash-mixers from the Python Package Index.

Usage

Command-line plugin subcommands can be listed by:

sourmash scripts

and detailed usage information for each plugin command can be seen with

sourmash scripts <command> -h

e.g. sourmash scripts sketchall -h.

You can list all installed plugins with:

sourmash info -v

Developer information

If you're interested in developing your own plugin, or updating an existing plugin, please see sourmash plugins via Python entry points. A template repository is available there for people who want to just get started writing code! Or you can get started with any of the plugins described above!

For questions, comments, and help writing and testing plugins, please file issues over on sourmash-bio/sourmash and/or visit our gitter/matrix channel.

Some back story on plugins - their motivation, and their implementation - can be found in this blog post.

If you're interested in adding your own plugin to sourmash-mixers specifically, please create a new issue in the sourmash-mixers repository with "Checklist for a new plugin" and fill it out as you can, and then ask for more instructions on that issue!