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.
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:¶
- 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
sourmash
Python 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 -
scaled
andnum
- Working with indexed collections of signatures
- Using the
LCA_Database
API - Using
sourmash
output with R and other languages