CIBIG 2026 — Python for Bioinformatics
Datasets for the practicals
======================================

Unpack this archive at the root of the course folder, so that you end up with:

    python_on_bioinformatics/
    ├── chapters/
    ├── exercises/
    ├── data/          <-- this folder
    └── ...

    tar xzf cibig2026_data.tar.gz

Contents
--------

Algae genotyping case study, used from day 1 to day 3:

  all_samples.vcf.gz        variant calls, 1 378 175 variants, 18 samples
  metadata_algae.tsv        28 strains: species, site, coordinates, depth, date
  algea_flagstats/          samtools flagstat reports, one per sample
  algae/                    GCA_002220235.gff, genome annotation (appendix)

Teaching datasets for the day 1 practicals:

  Germinal.txt              text file, reading and filtering lines
  Zola.txt                  text file, extracting headers
  fichier_tabulate.tsv      tabulated file, computing a sum column
  countries_cities.tsv      tabulated file, reading options
  cities.csv                comma-separated file, used in the pandas chapter
  filename.txt              three-line file, used in the chapter on files
  pyfiles.py                program to modify in the last practical

Note
----

strains.tsv and sites.tsv are NOT in this archive: you produce them yourself,
in the pandas chapter, by splitting metadata_algae.tsv.
