Tutorials and examples

These tutorials are 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.

• Installing sourmash with conda

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

• Using sourmash LCA to do taxonomic classification

• Analyzing the genomic and taxonomic composition of an environmental genome using GTDB and sample-specific MAGs with sourmash

• Some sourmash command line examples!

How-To Guides

• Classifying genome and metagenome sketches

• A quickstart guide to using RocksDB indexing

• Working with private collections of genome sketches

• Using the LCA_Database API

• Building plots from sourmash compare output.

• A short guide to using sourmash output with R.

Frequently Asked Questions

• Frequently asked questions

How sourmash works under the hood

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

• Support, versioning, and migration between versions

Reference material

• UNIX command-line documentation

• Genbank and GTDB databases and taxonomy files

• Python examples using the API

• Publications about sourmash

• A guide to the internal design and structure of sourmash

• Funding acknowledgements

Developing and extending sourmash

• Getting started with sourmash development

• Releasing a new version of sourmash

Full table of contents for all docs