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.
Background and details¶
These next three tutorials are all notebooks that you can view, run yourself, or run interactively online via the binder service.
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
which produces comparison matrices and dendrograms, please see
Building plots from
sourmash compare output.
- The first sourmash tutorial - making signatures, comparing, and searching
- Using sourmash LCA to do taxonomic classification
- An introduction to k-mers for genome comparison and analysis
- Some sourmash command line examples!
- sourmash: working with private collections of signatures
sourmashPython API examples
- A first example: two k-mers
- Introduction: k-mers, molecule types, and hashing.
- Set operations on hashes
- Creating MinHash sketches programmatically, from genome files
- Plotting dendrograms and matrices
- Saving and loading signature files
- Going from signatures back to MinHash objects and their hashes -
- Advanced features of sourmash MinHash objects -
- Working with indexed collections of signatures
- Using the
sourmashoutput with R and other languages