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mkdocs.yml
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site_name: Markdown Manuals for Bioinformatics Training Platform (BTP)
site_description: This contains all material for Markdown version of BTP workshops.
site_author: Authors
#site_url: 'https://bpa-csiro-workshops.github.io/btp-manuals-md'
copyright: '© The authors; 2017-'
#Documentation and theme
theme: material
# Options
extra:
palette:
primary: 'indigo'
accent: 'light blue'
feature:
tabs: true
logo: 'media/logos/bpalogo.png'
site_favicon: 'media/logos/bpalogo.png'
# social:
# - type: github
# link: https://bpa-csiro-workshops.github.io/btp-manuals-md
markdown_extensions:
- admonition
- smarty
- tables
- markdown_include.include
- codehilite:
linenums: True
- toc:
permalink: True
- mdx_math
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.critic
- pymdownx.inlinehilite
- pymdownx.magiclink
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.superfences
- pymdownx.tasklist:
custom_checkbox: True
- pymdownx.tilde
- pymdownx.details
extra_css:
#- css/extra.css
- css/details.css
extra_javascript:
- https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML
- js/details.js
nav:
- Home: index.md
- The Trainers: trainers/trainers.md
- Timetable:
- Intro to NGS: timetables/timetable_introNGS.md
- Cancer Genomics: timetables/timetable_cancer.md
- Long Read: timetables/timetable_longRead.md
- Workshop Information: preamble.md
# - All Modules:
# - ChIP-seq: modules/btp-module-chip-seq/chip-seq.md
# - DeNovo Canu: modules/btp-module-denovo-canu/denovo_canu.md
# - NGS Biological Insight: modules/btp-module-ngs-bio/biol.md
# - NGS Introduction to Command Line: modules/btp-module-ngs-cli/commandline.md
# - NGS Read Alignment: modules/btp-module-ngs-mapping/alignment.md
# - NGS Data Quality: modules/btp-module-ngs-qc/ngs-qc.md
# - RNA-Seq: modules/btp-module-rna-seq/rna-seq.md
# - de novo Genome Assembly with Velvet: modules/btp-module-velvet/velvet.md
# - Cancer Read Alignment: modules/cancer-module-alignment/alignment.md
# - Copy Number Variation: modules/cancer-module-cnv/cnv-tut.md
# - Single Nucleotide Variant Calling and Annotation: modules/cancer-module-snv/snv.md
# - Somatic Mutations:
# - Assessing somatic mutational signatures: modules/cancer-module-somatic/01_signatures.md
# - Cohort analysis for the identification of driver genes: modules/cancer-module-somatic/02_intogen.md
# - Structural Variant Analysis: modules/cancer-module-sv/sv_tut.md
# - Cancer Variant Visualisation: modules/cancer-module-viz/visu.md
# - Bacterial Assembly: modules/denovo-module-bac/bac_asm.md
# - DeNovo Introduction to Command Line: modules/denovo-module-cli/commandline.md
# - Eukaryote Assembly: modules/denovo-module-euk/eukaryotic_assem.md
# - Scaffolding: modules/denovo-module-scaffolding/scaffold.md
# - Metagenomics Functional Analysis:
# - Functional Analysis using EMG: modules/metagenomics-module-fda/fda.md
# - Metagenomics mining EMG with R:
# - Mining EMG with R part 1: modules/metagenomics-module-emgr/emgr-part1.md
# - Mining EMG with R part 2A: modules/metagenomics-module-emgr/emgr-part2A.md
# - Mining EMG with R part 2B: modules/metagenomics-module-emgr/emgr-part2B.md
# - Metagenomics Data Quality: modules/metagenomics-module-qc/ngs-qc.md
# - Metagenomics Taxonomic : modules/metagenomics-module-tax/tax.md
# - Metagenomics Visualisation: modules/metagenomics-module-vis/vis.md
# - Metagenomics WGA: modules/metagenomics-module-wga/wga.md
- Introduction to NGS Modules:
- Introduction to Command Line: modules/btp-module-ngs-cli/commandline.md
- Data Quality: modules/btp-module-ngs-qc/ngs-qc.md
- Read Alignment: modules/btp-module-ngs-mapping/alignment.md
- ChIP-seq: modules/btp-module-chip-seq/chip-seq.md
- RNA-Seq: modules/btp-module-rna-seq/rna-seq.md
- NGS Biological Insight: modules/btp-module-ngs-bio/biol.md
- de novo Genome Assembly: modules/btp-module-velvet/velvet.md
- DeNovo Canu: modules/btp-module-denovo-canu/denovo_canu.md
- Cancer Genomics Modules:
- Read Alignment: modules/cancer-module-alignment/alignment.md
- Single Nucleotide Variant Calling and Annotation: modules/cancer-module-snv/snv.md
- Copy Number Variation: modules/cancer-module-cnv/cnv-tut.md
- Structural Variant Analysis: modules/cancer-module-sv/sv_tut.md
- Variant Visualisation: modules/cancer-module-viz/visu.md
- Somatic Mutations:
- Assessing somatic mutational signatures: modules/cancer-module-somatic/01_signatures.md
- Cohort analysis for the identification of driver genes: modules/cancer-module-somatic/02_intogen.md
- DeNovo Modules:
# - DeNovo Command Line: modules/denovo-module-cli/commandline.md
- Bacterial Assembly: modules/denovo-module-bac/bac_asm.md
- Eukaryote Assembly: modules/denovo-module-euk/eukaryotic_assem.md
- Scaffolding: modules/denovo-module-scaffolding/scaffold.md
- Metagenomics Modules:
- Metagenomics QC: modules/metagenomics-module-qc/ngs-qc.md
- Metagenomics Taxonomic: modules/metagenomics-module-tax/tax.md
- Metagenomics Visualisation: modules/metagenomics-module-vis/vis.md
- Metagenomics WGA: modules/metagenomics-module-wga/wga.md
- Metagenomics Functional Analysis: modules/metagenomics-module-fda/fda.md