Repository for the AGB 2025 common class project
Wiki you can modify and use to document the process!
In this wiki page you will find the information about the pipeline context, the sample processing and the decisions made through each of the modules (https://github.com/egenomics/agb2025/wiki/Pipeline-Context).
├── 📁 raw_data/ # Original FASTQ files (paired-end reads)
│ ├── sample1_R1.fastq.gz
│ ├── sample1_R2.fastq.gz
│ └── ...
├── 📁 metadata/ # Sample metadata (CSV or TSV)
│ └── run_metadata.csv
├── 📁 scripts/ # Custom or pipeline scripts
│ └── …
├── 📁 outputs/ # Outputs per run
│ └── 📁 run_YYYYmmdd_hhmmss
│ ├── 📁 qc_reports/ # FastQC or MultiQC reports
│ │ ├── fastqc/
│ │ └── multiqc_report.html
│ ├── 📁 processed_data/ # Trimmed, filtered reads
│ │ ├── data_filtered/
│ │ └── qiime2_demux/
│ ├── 📁 feature_tables/ # OTU or ASV tables
│ │ ├── table.qza
│ │ └── table.tsv
│ ├── 📁 taxonomy/ # Taxonomy assignment results
│ │ ├── classifier.qza
│ │ ├── taxonomy.qza
│ │ └── taxonomy.tsv
│ ├── 📁 phylogeny/ # Phylogenetic tree files
│ │ ├── rooted-tree.qza
│ │ └── unrooted-tree.qza
│ ├── 📁 diversity_analysis/ # Alpha & beta diversity
│ │ ├── core-metrics-results/
│ │ └── emperor_plots/
│ └── 📁 visualizations/ # QIIME 2 visualizations
│ ├── taxonomy_barplots.qzv
│ ├── rarefaction_curves.png
│ └── …
├── 📁 results/ # Final summary tables and plots per run (or sample?)
│ └── summary_report.html
│
└── 📁 logs/ # Pipeline logs
└── run_YYYYmmdd_hhmmss_pipeline.log