dada2-rs/mkdocs.yml at main · HPCBio/dada2-rs · GitHub

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site_name: dada2-rs
site_description: An experimental Rust implementation of DADA2
site_author: HPCBio
repo_url: https://github.com/HPCBio/dada2-rs
repo_name: HPCBio/dada2-rs
edit_uri: edit/main/docs/

theme:
  name: material
  features:
    - navigation.sections
    - navigation.top
    - navigation.tracking
    - content.code.copy
    - search.suggest
    - toc.follow
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/weather-sunny
        name: Switch to light mode

markdown_extensions:
  - admonition
  - tables
  - attr_list
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.arithmatex:
      generic: true
  - toc:
      permalink: true

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

nav:
  - Home: index.md
  - About: about.md
  - Building & installing: installation.md
  - Algorithm:
    - Denoising modes: algorithm.md
    - Shared denoising core: algorithm-core.md
    - Per-sample (dada): algorithm-dada.md
    - Pooled (dada-pooled): algorithm-dada-pooled.md
    - Pseudo-pooled (dada-pseudo): algorithm-dada-pseudo.md
  - Walkthroughs:
    - Illumina MiSeq: walkthroughs/walkthrough-illumina.md
    - Illumina - Binned Quality: walkthroughs/walkthrough-illumina-binned.md
    - PacBio HiFi: walkthroughs/walkthrough-pacbio.md
    - PacBio - Binned Quality: walkthroughs/walkthrough-pacbio-binned.md
  - Parameters: parameters.md
  - Performance:
    - Tuning for your data: tuning-for-your-data.md
    - Tooling & metrics: benchmarking.md
    - Results: results.md
  - Findings:
    - Overview: findings/index.md
    - KDIST cutoff decoupling: findings/kdist-cutoff-decoupling.md
    - K-mer screen size: findings/kmer-size-screening.md
    - Band size & platform defaults: findings/band-size-platform-defaults.md
    - Carrying compmax across buds: findings/shuffle-compmax-carry.md
    - Redesigning b_shuffle (closed): findings/shuffle-build-scan.md
    - Inside b_compare — screen vs align: findings/compare-screen-vs-align.md
    - Inside b_compare — the serial remainder: findings/compare-serial-fold.md
    - Inside b_compare — the store scan: findings/compare-store-scan.md
    - Measuring on a NUMA node: findings/measuring-on-numa.md
    - Thread scaling & memory placement: findings/thread-scaling-and-placement.md
    - Pseudo-pooling priors vs error model: findings/pseudo-pooling-priors-vs-error-model.md
    - Binned quality scores:
      - Overview: findings/binned-quality.md
      - PacBio (SequelIIe & Revio): findings/binned-quality-error-model.md
      - Illumina NovaSeq 6000 (16S): findings/binned-quality-illumina-novaseq.md
      - Illumina NovaSeq 6000 (ITS2): findings/binned-quality-illumina-its2.md
      - Reading the prep first: findings/reading-the-prep.md
  - Diagnostics: diagnostics.md
  - Citation: citation.md