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sourmash_plugin_branchwater

PyPI Conda Version

tl;dr Do faster and lower-memory sourmash functions via this plugin.

Details

sourmash is a command-line tool and Python/Rust library for metagenome analysis and genome comparison using k-mers. While sourmash is fast and low memory, sourmash v4 and lower work in single-threaded mode with Python containers.

The branchwater plugin for sourmash (this plugin!) provides faster and lower-memory implementations of several important sourmash features - sketching, searching, and gather (metagenome decomposition). It does so by implementing higher-level functions in Rust on top of the core Rust library of sourmash. As a result it provides some of the same functionality as sourmash, but 10-100x faster and in 10x lower memory.

This code is still in prototype mode, and does not have all of the features of sourmash. As we add features we will move it back into the core sourmash code base; eventually, much of the code in this repository will be integrated into sourmash directly.

If you're intrigued but not sure where to start with this plugin, we suggest first identifying what sourmash functionality you need to run to accomplish your goals. Once you have your sourmash commands working, revisit these docs and see if there is a faster implementation available in this plugin!

This repo originated as a PyO3-based Python wrapper around the core branchwater code. Branchwater is a fast, low-memory and multithreaded application for searching very large collections of FracMinHash sketches as generated by sourmash.

For technical details, see the Rust code in src/ and Python wrapper in src/python/.

Documentation

There is a quickstart below, as well as more user documentation here. Nascent developer docs are also available!

The betterplot plugin supplies a number of commands that work with branchwater output. In particular,

  • mds2 and tsne2 generate MDS and tSNE plots from pairwise output;
  • clustermap1 generates seaborn clustermaps from pairwise and multisearch output;
  • clusters_to_categories uses the output of the cluster command to generate categories for coloring and labeling plots;
  • pairwise_to_matrix converts the output of pairwise to a sourmash comparison matrix;

See the betterplot README for example figures and commands!

Quickstart demonstrating multisearch.

This quickstart demonstrates multisearch using the 64 genomes from Awad et al., 2017.

1. Install the branchwater plugin

On Linux and Mac OS X, you can install the latest release of the branchwater plugin from conda-forge:

conda install sourmash_plugin_branchwater

Please see the developer docs for information on installing the latest development version.

2. Download sketches.

The following commands will download sourmash sketches for the podar genomes into the file podar-ref.zip:

curl -L https://osf.io/4t6cq/download -o podar-ref.zip

3. Execute!

Now run multisearch to search all the sketches against each other:

sourmash scripts multisearch podar-ref.zip podar-ref.zip -o results.csv --cores 4

You will (hopefully ;)) see a set of results in results.csv. These are comparisons of each query against all matching genomes.

Debugging help

If your collections aren't loading properly, try running sourmash sig summarize on them, like so:

sourmash sig summarize podar-ref.zip

If this doesn't work, then you're running into problems creating the collection. Please ask for help on the sourmash issue tracker!

Code of Conduct

This project is under the sourmash Code of Conduct.

License

This software is under the AGPL license. Please see LICENSE.txt.

Authors

  • Luiz Irber
  • C. Titus Brown
  • Mohamed Abuelanin
  • N. Tessa Pierce-Ward
  • Olga Botvinnik