https://github.com/bu-isciii/bacterial_wgs_training
In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
https://github.com/bu-isciii/bacterial_wgs_training
bacterial-genomes bacterial-wgs-training genome nextflow ngs-analysis outbreak-detection outbreaks sequencing wgs wgs-analysis
Last synced: 2 months ago
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In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
- Host: GitHub
- URL: https://github.com/bu-isciii/bacterial_wgs_training
- Owner: BU-ISCIII
- License: gpl-3.0
- Created: 2018-09-20T09:01:00.000Z (about 7 years ago)
- Default Branch: four_days_format
- Last Pushed: 2024-10-31T08:18:20.000Z (12 months ago)
- Last Synced: 2025-07-04T08:40:41.385Z (4 months ago)
- Topics: bacterial-genomes, bacterial-wgs-training, genome, nextflow, ngs-analysis, outbreak-detection, outbreaks, sequencing, wgs, wgs-analysis
- Language: HTML
- Homepage:
- Size: 166 MB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
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# Bacterial WGS training
In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
The material includes slides with theory concepts and a bunch of practical exercises using nextflow and singularity, focusing on the interpretation of results.
## Agenda
### Day 1
- **Talk 1 and 2:** [Massive sequencing of bacterial genomes. State-of-the-art. & Bacterial genomes sequencing. Applications.](slides/talk1/20241028_6ED_curso_SeqGenBac_session1.1-2_Introduccion_EAB.pdf)
- **Talk 3:** [The computing revolution in Biosciences. Nextflow and Singularity introduction.](slides/talk3/curso_SeqGenBac_ChangingComputingParadigm.pdf)
- **Talk 4:** [Linux environment review.](slides/talk2/curso_SeqGenBac_session1.2_linux.pdf)
- [**Exercise 0**](exercises/00_SetUp.md) -- [Download pdf](exercises/00_SetUp.pdf)
- [**Exercise 1**](exercises/01_LinuxBasicCommands.md) -- [Download pdf](exercises/01_LinuxBasicCommands.pdf)
- [**Exercise 2**](exercises/02_NextflowSingularity.md) -- [Download pdf](exercises/02_LinuxNextflowSingularity.pdf)
### Day 2
- **Talk 5:** [Quality analysis and control of HTS data](slides/talk5/curso_SeqGenBac_session2.2_quality_assesment.pdf)
- **Talk 6:** [Bacterial genomes assembly](slides/talk6/slidestalk620221017_5ED_curso_SeqGenBac_session2.3_assembly_ICuesta.pdf.pdf)
- **Talk 7:** [Sequence annotation](slides/talk11/20231020_5ED_curso_SeqGenBac_session5.1_annotation_ICuesta.pdf)
- [**Exercise 3**](exercises/03_QualityAndAssembly.md) -- [Download pdf](exercises/03_QualityAndAssembly.pdf)
### Day 3
- **Talk 8:** [Mapping against reference genome and Variant Calling.](slides/talk7/curso_SeqGenBac_session3.1_MappingAndVariantCalling.pdf)
- **Talk 9:** [SNP matrix and phylogenetics.](slides/talk8/curso_SeqGenBac_session3.2_SNPMatrixAndPhylogenetics.pdf)
- [**Exercise 4**](exercises/04_outbreakSNP.md) -- [Download pdf](exercises/04_outbreakSNP.pdf)
### Day 4
- **Talk 10:** [Typing based on allelic profile or gene-by-gene](slides/talk10/20231019_5ED_curso_SeqGenBac_session4.1_tipificacion-gen-by-gene_ICuesta.pdf)
- **Talk 11:** [Gene-by-gene WGS analysis](slides/talk10/curso_SeqGenBac_session4.2_GeneByGenevsSNPs.pdf)
- [**Exercise 5**](./exercises/05_outbreakcgMLST.md) -- [Download pdf](exercises/05_outbreakcgMLST.pdf)
- [**Exercise 6**](exercises/06_annotation.md) -- [Download pdf](exercises/06_annotation.pdf)