Deploying to gh-pages from @ 09afdc8 🚀

cambiotraining · Mar 12, 2024 · d9cf4ee · d9cf4ee
commit d9cf4ee
Show file tree

Hide file tree

Showing 84 changed files with 70,746 additions and 0 deletions.
diff --git a/.nojekyll b/.nojekyll
diff --git a/index.html b/index.html
diff --git a/materials/01-intro/01-surveillance.html b/materials/01-intro/01-surveillance.html
diff --git a/materials/01-intro/02-ngs.html b/materials/01-intro/02-ngs.html
diff --git a/materials/01-intro/03-workflows.html b/materials/01-intro/03-workflows.html
diff --git a/materials/01-intro/images/Ct_coverage_relationship.png b/materials/01-intro/images/Ct_coverage_relationship.png
diff --git a/materials/01-intro/images/artic_protocol.png b/materials/01-intro/images/artic_protocol.png
diff --git a/materials/01-intro/images/fastqc_quality.png b/materials/01-intro/images/fastqc_quality.png
diff --git a/materials/01-intro/images/gisaid_metadata.png b/materials/01-intro/images/gisaid_metadata.png
diff --git a/materials/01-intro/images/igv_overview.svg b/materials/01-intro/images/igv_overview.svg
diff --git a/materials/01-intro/images/lineages_example.svg b/materials/01-intro/images/lineages_example.svg
diff --git a/materials/01-intro/images/metagenomic_vs_amplicon.svg b/materials/01-intro/images/metagenomic_vs_amplicon.svg
diff --git a/materials/01-intro/images/multiqc.svg b/materials/01-intro/images/multiqc.svg
diff --git a/materials/01-intro/images/ngs_mapping.svg b/materials/01-intro/images/ngs_mapping.svg
diff --git a/materials/01-intro/images/virus-RT-qPCR.png b/materials/01-intro/images/virus-RT-qPCR.png
diff --git a/materials/02-isolates/01-consensus.html b/materials/02-isolates/01-consensus.html
diff --git a/materials/02-isolates/02-qc.html b/materials/02-isolates/02-qc.html
diff --git a/materials/02-isolates/03-lineages.html b/materials/02-isolates/03-lineages.html
diff --git a/materials/02-isolates/04-phylogeny.html b/materials/02-isolates/04-phylogeny.html
diff --git a/materials/02-isolates/images/alignment_aliview.png b/materials/02-isolates/images/alignment_aliview.png
diff --git a/materials/02-isolates/images/igv_amplicon_dropout.svg b/materials/02-isolates/images/igv_amplicon_dropout.svg
diff --git a/materials/02-isolates/images/igv_deletion_example.svg b/materials/02-isolates/images/igv_deletion_example.svg
diff --git a/materials/02-isolates/images/lineages_example.svg b/materials/02-isolates/images/lineages_example.svg
diff --git a/materials/02-isolates/images/nextclade_deletion_example.svg b/materials/02-isolates/images/nextclade_deletion_example.svg
diff --git a/materials/02-isolates/images/nextclade_overview.svg b/materials/02-isolates/images/nextclade_overview.svg
diff --git a/materials/02-isolates/images/phylogeny_figtree.svg b/materials/02-isolates/images/phylogeny_figtree.svg
diff --git a/materials/02-isolates/images/switzerland_variants.svg b/materials/02-isolates/images/switzerland_variants.svg
diff --git a/materials/02-isolates/images/variants_snps_indels.svg b/materials/02-isolates/images/variants_snps_indels.svg
diff --git a/materials/02-isolates/images/viralrecon_coverage_heatmap.png b/materials/02-isolates/images/viralrecon_coverage_heatmap.png
diff --git a/materials/02-isolates/images/viralrecon_multiqc_plot.png b/materials/02-isolates/images/viralrecon_multiqc_plot.png
diff --git a/materials/02-isolates/images/viralrecon_multiqc_variant_metrics.svg b/materials/02-isolates/images/viralrecon_multiqc_variant_metrics.svg
diff --git a/materials/02-isolates/images/viralrecon_pipeline_info_duration.png b/materials/02-isolates/images/viralrecon_pipeline_info_duration.png
diff --git a/materials/02-isolates/images/viralrecon_workflow_illumina.svg b/materials/02-isolates/images/viralrecon_workflow_illumina.svg
diff --git a/materials/02-isolates/images/viralrecon_workflow_medaka.svg b/materials/02-isolates/images/viralrecon_workflow_medaka.svg
diff --git a/materials/02-isolates/images/workflow_overview.svg b/materials/02-isolates/images/workflow_overview.svg
diff --git a/materials/03-case_studies/01-switzerland.html b/materials/03-case_studies/01-switzerland.html
diff --git a/materials/03-case_studies/02-southafrica.html b/materials/03-case_studies/02-southafrica.html
diff --git a/materials/03-case_studies/03-eqa.html b/materials/03-case_studies/03-eqa.html
diff --git a/materials/03-case_studies/images/analysis_overview.png b/materials/03-case_studies/images/analysis_overview.png
diff --git a/materials/03-case_studies/images/civet_catchment_example.png b/materials/03-case_studies/images/civet_catchment_example.png
diff --git a/materials/03-case_studies/images/precision_sensitivity.svg b/materials/03-case_studies/images/precision_sensitivity.svg