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  5. Module 1.2 materials

GenEpi-BioTrain - Training Materials on Genomic Epidemiology and Public Health Bioinformatics - Bridging the gaps

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Module 1.2 materials

    • Bash_Exercises.pdfBash_Exercises.pdf
    • Bash_Handout.pdfBash_Handout.pdf
    • Bash_Presentation_2025.pptxBash_Presentation_2025.pptx
    • Commandline_Answers.pdfCommandline_Answers.pdf
    • day1.tar.gzday1.tar.gz
    • Presentation_commandline.pptxPresentation_commandline.pptx
    • SolutionsForBash.shSolutionsForBash.sh
    • Unix_Exercises.pdfUnix_Exercises.pdf
    • Unix_Handout.pdfUnix_Handout.pdf
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GenEpi-BioTrain - Training Materials on Genomic Epidemiology and Public Health Bioinformatics - Bridging the gaps

  • Participants

  • Training materials for facilitators

  • Overview

  • Training Materials

    • FileOnline orientation session for participants (2 we...

    • PageCreate user-account on ENA

    • FileUnix Handout

    • PageModule 1.1 Course introduction (outline)

    • FolderModule 1.1 materials

    • PageModule 1.2 Introduction to Linux and Bash (outline)

    • FolderModule 1.2 materials

    • PageModule 1.3 Getting started with python (outline)

    • FolderModule 1.3 materials

    • PageModule 1.4a Advancing in programming (outline)

    • FolderModule 1.4a materials

    • PageModule 1.4b Coding best practice 2023 (outline)

    • FolderModule 1.4b materials

    • PageModule 2.1 Sequencing and raw-data QC (outline)

    • FolderModule 2.1 materials

    • URLQuality Control of Raw read data

    • PageModule 2.2 Introduction to genome assembly (outline)

    • FolderModule 2.2 materials

    • PageModule 2.3a Short-read genome assembly and QC

    • FolderModule 2.3a materials

    • PageModule 2.3b Reference-based assembly (SARS-Cov-2/I...

    • FolderModule 2.3b materials

    • PageModule 2.4 Long-read and hybrid de novo genome ass...

    • FolderModule 2.4 materials

    • PageModule 3.1 Blast, in silico MLST and gene annotati...

    • FolderModule 3.1 materials

    • PageModule 3.2 - Getting started with phylogenies (out...

    • FolderModule 3.2 materials

    • PageModule 3.3a - Pathogen-wave oriented analyses 2023...

    • FolderModule 3.3a materials

    • PageModule 3.3b - Pathogen-wave oriented analyses 2024...

    • FolderModule 3.3b materials

    • PageModule 3.3c - Pathogen-wave oriented analyses 2025...

    • FolderWGS-based detection of antimicrobial resistance (A...

    • FolderTuberculosis profiling

    • PageModule 3.4 - Data sharing (outline)

    • FolderModule 3.4 materials

    • PageModule 3.5 Online tools for genetic analysis (outl...

    • FolderModule 3.5 materials

    • PageModule 4.1 Pipeline development (outline)

    • URLBacterial Genome Assembly - Advanced (For the Inde...

    • URLBacterial genome assebmly - Intermediate (Exercise...

    • URLBacterial Genome Assembly - VERY Basic (Exercise i...

    • FolderModule 4.1 Old materials

    • PageModule 4.2 Automation – going large-scale (outline)

    • FolderModule 4.2 materials

    • PageModule 5.1 - What's next (outline)

    • Fileoutlook continued learning

    • FolderAdditional Resources - Scripts developed by trainers

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