The guix-bioinformatics README.org now has a comprehensive overview with three tables:

  1. Pangenome tools -- 33 packages in the pangenomes meta-package
  2. MEMPANG workshop -- additional R, Python, and utility packages
  3. GeneNetwork packages -- 9 GN-specific packages

1 files changed, 67 insertions, 1 deletions

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 IMPORTANT: this repository lives at https://git.genenetwork.org/guix-bioinformatics/!
 Older packages have been moved to https://git.genenetwork.org/guix-bioinformatics-past/.
 
-Over 400 bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places.
+Over 300 bioinformatics packages for Guix that are used in https://genenetwork.org/ and some other places.
 Mostly targetting genomics, pangenomics and genetics.
 
+** Pangenome tools (pangenomes meta-package)
+
+The =pangenomes= meta-package provides a comprehensive pangenomics toolkit:
+
+| Tool           | Version      | Description                                    |
+|----------------+--------------+------------------------------------------------|
+| pggb           | 0.7.4        | PanGenome Graph Builder pipeline               |
+| wfmash         | 0.14.0       | Whole-genome Fuzzy Mapping and Alignment        |
+| seqwish        | 0.7.11       | Sequence graph induction from alignments        |
+| smoothxg       | 0.8.2        | Graph normalization via partial order alignment  |
+| odgi           | 0.9.0        | Optimized Dynamic Genome/Graph Implementation   |
+| vg             | 1.72.0       | Variation graph toolkit                         |
+| impg           | 0.4.1        | Implicit pangenome graph queries                |
+| minimap2       | 2.28         | Fast pairwise aligner (from Guix upstream)      |
+| bwa-mem2       | 2.3          | Burrows-Wheeler Aligner for short reads         |
+| samtools       | 1.19         | SAM/BAM/CRAM manipulation (from Guix upstream)  |
+| htslib         | 1.21         | HTSlib C library (from Guix upstream)           |
+| bedtools       | 2.31.1       | Genome interval tools (from Guix upstream)      |
+| bcftools       | 1.21         | VCF/BCF manipulation (from Guix upstream)       |
+| vcflib         | 1.0.15       | VCF manipulation library and tools              |
+| vcfbub         | 0.1.0        | VCF bubble popping                              |
+| bandage-ng     | 2026.4.1     | Assembly graph visualizer (Qt6)                 |
+| gfalook        | 0.1.0        | GFA visualization (odgi viz reimplementation)   |
+| pafplot        | 0.1.0        | PAF alignment dotplot renderer                  |
+| wally          | 0.7.1        | Structural variant visualization                |
+| agc            | 2.1          | Assembled Genomes Compressor                    |
+| cigzip         | 0.1.0        | CIGAR compression with tracepoints              |
+| cosigt         | 0.1.7        | Pangenome haplotype genotyping                  |
+| gfainject      | 0.1.0        | BAM-to-GAF graph injection                      |
+| gafpack        | 0.0.0        | GAF coverage vector extraction                  |
+| gfaffix        | 0.2.1        | Walk-preserving graph simplification            |
+| gfautil        | 0.4.0        | GFA format utilities                            |
+| fastga-rs      | 0.1.2        | Fast genome aligner (Rust)                      |
+| fastix         | 0.1.0        | FASTA header prefix renaming (PanSN)            |
+| kfilt          | 0.1.1        | K-mer filtering                                 |
+| meryl          | 1.4.1        | K-mer counting and set operations               |
+| miniprot       | 0.18         | Protein-to-genome aligner                       |
+| pangene        | 1.1          | Gene-level pangenome analysis                   |
+| rtg-tools      | 3.13         | VCF evaluation (vcfeval)                        |
+
+** MEMPANG workshop (mempang-workshop meta-package)
+
+Extends =pangenomes= with R plotting, Python, and general utilities
+for the MEMPANG pangenome workshop tutorials:
+
+| Category       | Packages                                             |
+|----------------+------------------------------------------------------|
+| R packages     | r-ggplot2, r-tidyverse, r-ape, r-ggtree, r-gggenes  |
+| Python         | python, python-igraph, python-pycairo                |
+| Utilities      | graphviz, gnuplot, parallel, pigz, wget, zstd, bc    |
+| QC             | multiqc, mummer                                      |
+
+** GeneNetwork packages
+
+| Package              | Version      | Description                           |
+|----------------------+--------------+---------------------------------------|
+| genenetwork2         | 3.11         | GeneNetwork2 web application          |
+| genenetwork3         | 0.1.0        | GeneNetwork3 REST API                 |
+| gn-auth              | 1.0.1        | GN authentication service             |
+| gn-guile             | 4.0.0        | Guile utilities for GN                |
+| gn-libs              | 0.0.0        | Shared Python libraries               |
+| gn-uploader          | 0.1.1        | Data uploader                         |
+| gemma-wrapper        | 0.99.6       | GEMMA CLI wrapper                     |
+| gemma-gn2            | 0.98.5       | GEMMA for GeneNetwork2                |
+| genecup              | 1.8          | GeneCup literature mining             |
+
 See Guix documentation and [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for installing and hacking Guix.
 
 See [[https://github.com/franzos/awesome-guix][awesome guix]] for a list of other channels.