tutorials.md

sourmash tutorials and notebooks

The first two tutorials!

These tutorials are both command line tutorials that should work on Mac OS X and Linux. They require about 5 GB of disk space and 5 GB of RAM.

• The first sourmash tutorial - making signatures, comparing, and searching

• Using sourmash LCA to do taxonomic classification

Background and details

These next three tutorials are all notebooks that you can view, run yourself, or run interactively online via the binder service.

• An introduction to k-mers for genome comparison and analysis

• Some sourmash command line examples!

• Working with private collections of signatures.

More information

If you are a Python programmer, you might also be interested in our API examples as well as a short guide to Using the LCA_Database API.

If you prefer R, we have a short guide to using sourmash output with R.

Customizing matrix and dendrogram plots in Python

If you're interested in customizing the output of sourmash plot, which produces comparison matrices and dendrograms, please see Building plots from sourmash compare output.

Contents:

:maxdepth: 2

tutorial-basic
tutorials-lca
kmers-and-minhash
sourmash-examples
sourmash-collections
api-example
using-LCA-database-API
other-languages