mkdocs.yml

site_name: Bioinformatics course

theme:
  name: cinder

nav:
  - Home: index.md
  - First week:
      - Blast Online: blast/blast_online.md
      - Unix: unix.md
      - Cloud Computing: cloud.md
      - Command-line Blast: blast/blast_cli.md
  - Second week:
      - Sequencing Technologies: seq_tech.md
      - Quality Control: tutorials/docs/qc.md
      - De-novo Genome Assembly: tutorials/docs/assembly.md
      - Assembly Challenge: assembly_challenge.md
      - Genome Annotation: tutorials/docs/annotation.md
      - Pan-genome Analysis: tutorials/docs/pan_genome.md
      - Nanopore Sequencing: tutorials/docs/nanopore.md
  - Week 3:
      - Sequencing Technologies: seq_tech.md
      - Quality Control: tutorials/docs/qc.md
      - Assembly Challenge: assembly_challenge.md
      - De-novo Genome Assembly: tutorials/docs/assembly.md
      - Genome Annotation: tutorials/docs/annotation.md
      - Pan-genome Analysis: tutorials/docs/pan_genome.md
      - Nanopore Sequencing: tutorials/docs/nanopore.md
  - Week 4:
      - RNA Sequencing: tutorials/docs/rna.md
      - Eukaryotic Annotation:
        - Intro: nbis_annotation/schedule.md
        - Practical 1: nbis_annotation/practical_session/practical1.md
        - Practical 2: nbis_annotation/practical_session/practical2.md
        - Practical 3: nbis_annotation/practical_session/practical3_manualCuration.md
        - Practical 4: nbis_annotation/practical_session/practical4_funcAnnotInterp.md
        - WebApollo: nbis_annotation/practical_session/UsingWebApollo.md
        - Protein, EST and RNA-seq data: nbis_annotation/practical_session/practical2_sub_gatherEvidence.md
        - Assembling transcripts: nbis_annotation/practical_session/practical2_sub_transcriptome.md
        - Evidence Based Annotation: nbis_annotation/practical_session/practical2_sub_makerNoAbinit.md
        - Abinitio Annotation: nbis_annotation/practical_session/practical2_sub_makerAbinit.md
        - Comparing Annotations: nbis_annotation/practical_session/practical2_sub_makerCompareAnnot.md
        - Configuring Maker (I): nbis_annotation/practical_session/practical2_supl_maker.md
        - Configuring Maker (I): nbis_annotation/practical_session/practical2_supl3_maker.md
        - Inspecting Maker output: nbis_annotation/practical_session/practical2_supl2_maker.md
  - Week 5:
    - Metabarcoding: tutorials/docs/16S.md
    - Proteins: proteins.md
  - Week 6:
    - Metagenome assembly: tutorials/docs/meta_assembly.md
    - Comparative metagenomics: tutorials/docs/wms.md
    - Viral metagenomics: tutorials/docs/metavir.md

markdown_extensions:
  - admonition

extra_css:
  - css/admonition.css
  - css/navbar.css