Bioinformatics training materials

1. Analysis of High-Throughput RNA‑Seq Data

Quick start:

  • pixi + nextflow RNA‑Seq workflow
  • pixi + snakemake RNA‑Seq workflow

    • Overview: End‑to‑end RNA‑Seq workflow training covering raw FASTQ processing, QC, mapping, quantification, and differential expression.

    Tools included:

    • Nextflow + nf-core/rnaseq Or
    • Snakemake custom script
    • FastQC, MultiQC
    • STAR or HISAT2
    • featureCounts
    • DESeq2, clusterProfiler for GO/KO

    Results generated:

    • QC reports
    • Aligned BAM files
    • Count matrices
    • Differential expression tables
    • Functional enrichment plots
    2. Genome-Wide Predictions in Breeding (GWAS & GS)

    Training material: Genomic Prediction Workshop

    Overview: Hands‑on introduction to variant processing, GWAS pipelines, mixed models, and genomic prediction techniques.

    Tools included:

    • PLINK for SNP QC
    • GEMMA / MLMM for GWAS
    • R packages: rrBLUP, BGLR, sommer

    Results generated:

    • Filtered genotype sets
    • Manhattan/QQ plots
    • GWAS hit tables
    • Genomic Estimated Breeding Values (GEBVs)
    3. Data Handling & High‑Quality Figures in R

    Training material: Data Visualization in R

    Overview: Training on efficient data wrangling, multi‑table merging, and reproducible, publication-grade figure creation in R.

    Tools included:

    • tidyverse: dplyr, tidyr, readr
    • ggplot2 + patchwork
    • rmarkdown
    • GitHub for versioning

    Results generated:

    • Tidy & merged data structures
    • Statistical graphics
    • Multi-panel figures
    • Reproducible reports
    4. Multi‑omics Analysis of Microbial Communities

    Training material: Metagenomics & Multi‑omics Training

    Overview: End‑to‑end training covering metagenomic assembly, binning, taxonomy, and functional annotation.

    Tools included:

    • nf-core/mag
    • Kraken2 + Bracken
    • MetaBAT2, MaxBin
    • Prokka, eggNOG-mapper

    Results generated:

    • Taxonomic profiles
    • MAGs (assembled genomes)
    • Functional annotation reports
    • Pathway reconstructions
    5. Reproducible Bioinformatics, Nextflow & nf-core

    Training material: Reproducible Bioinformatics Workshop

    Overview: A fully hands‑on introduction to reproducible bioinformatics workflows using containers, CI, and modern pipeline design.

    Tools included:

    • Nextflow scripting
    • nf-core template + modules
    • Docker, Apptainer
    • GitHub Actions for CI

    Results generated:

    • Reusable Nextflow pipelines
    • Containerized reproducible environments
    • Automated CI testing
    • Releases with version tracking
    6. MedBioInfo — Medical Bioinformatics

    Training material: MedBioInfo Training Modules

    Overview: Modules covering biomedical data analysis, clinical genomics, multi‑omics, and statistical learning.

    Tools included:

    • R/Bioconductor workchains
    • Bash automation
    • Variant calling & annotation tools
    • Machine‑learning packages

    Results generated:

    • Clinical variant tables
    • DGE and expression matrices
    • Prediction model outputs
    • Exploratory and diagnostic plots
    Bioinformatics training materials compiled by SIB (GLITTR)

    Overview: This is a curated and actively maintained collection of bioinformatics training materials compiled by the Swiss Institute of Bioinformatics (SIB) and integrated into glittr.org.

    All resources in this collection are:

    • Free and openly accessible
    • Hosted on GitHub or GitLab
    • Written in Markdown or similar formats
    • Cover a wide range of bioinformatics topics

    Live README (auto-updated):

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    🔗 Visit GLITTR for the full interactive platform

    [def]: ttps://abu85.github.io/Pixi-in-bioinformatics/modules/nextflow_rnaseq_analysis.htm [def2]: ttps://abu85.github.io/nfcore_metagenomics_training