site_name: spacegraphcats documentation

site_url: http://spacegraphcats.github.io/spacegraphcats

repo_name: spacegraphcats

repo_url: https://github.com/spacegraphcats/spacegraphcats

edit_uri: ""

copyright: 'Copyright &copy; 2021 <a href="http://ivory.idyll.org/lab/">Lab for Data Intensive Biology</a> at UC Davis and <a href="https://www.cs.utah.edu/~sullivan/#!/">Theory in Practice Lab at University of Utah'

# change directory names here

docs_dir: doc

site_dir: site

theme:

name: material

# pretty colors! see https://squidfunk.github.io/mkdocs-material/getting-started/#primary-colors

palette:

primary: 'blue_grey'

accent: 'black'

# fun logos! see https://material.io/icons/

icon:

logo: material/share

font:

text: 'Roboto'

code: 'Roboto Mono'

# optionally give a title for each page or section

nav:

- "Primer on metagenomics and assembly graphs": "0a-primer.md"

- "Using spacegraphcats":

- "Installing spacegraphcats": "00-installing-spacegraphcats.md"

- "Running spacegraphcats": "01-running-spacegraphcats.md"

- "Spacegraphcats use cases": "02-spacegraphcats-use-cases.md"

- "Visualizing spacegraphcats outputs": "03-visualizing-spacegraphcats.md"

- "Tuning parameters in spacegraphcats": "04-spacegraphcats-parameters.md"

- "Alpha functionality in spacegraphcats": "05-alpha-spacegraphcats.md"

- "Integrating spacegraphcats into a snakemake workflow": "06-snakemake-spacegraphcats.md"

- "Calculating taxonomic purity of spacegraphcats outputs": "calculating-taxonomic-purity.md"

- "Developer's guide": "developing-spacegraphcats.md"