How liushuotong/oggi works
OGGI is a command-line toolkit for plant pangenome analyses. Its main workflow prepares assembly annotations and proteins, identifies target-family genes, evaluates local synteny, then compares clustering methods and reports candidate partitions. Separate branches construct BUSCO-based species trees, infer family HOGs from gene and species trees, and run whole-proteome OrthoFinder or standalone tool wrappers. The graph follows documented command-level workflows and sampled caller behavior; unsampled implementation details are represented only at supported module or directory paths.
Main entry points: oggi.py OGGI CLI · sub_collinearity.py Local synteny · hog_tree.py Family HOG inference · cluster_engine Cluster engine
Components 21
Family workflow
- OGGI CLI
oggi.py - Assembly reduction
reduce_rs - Family identification
gene_family_identification.py - Family FASTA and map
- Local synteny
sub_collinearity.py - Collinearity algorithms
collinearity.py - Collinear pairs
Trees and HOGs
- BUSCO assessment
busco_process.py - BUSCO results
- Species-tree inference
species_tree.py - Species tree
- Family HOG inference
cluster_engine/hog_tree.py - HOG algorithms
orthofinder_hog
Clustering and evaluation
- Cluster engine
cluster_engine - Partitions and reports
Tool integrations
- Whole-proteome OrthoFinder
orthofinder_process.py - OrthoFinder HOG import
cluster_engine/hog_import.py - Standalone wrappers
oggi.py
Other components
- Researcher
- Bioinformatics tools
- GFF and genome inputs
Connections 36
- Researcher → OGGI CLI: invokes
- GFF and genome inputs → OGGI CLI: provides inputs
- OGGI CLI → Assembly reduction: dispatches reduce
- Assembly reduction → Bioinformatics tools: uses AGAT tools
- Assembly reduction → Family identification: prepared assemblies
- OGGI CLI → Family identification: dispatches identify
- Family identification → Bioinformatics tools: searches with HMMER and DIAMOND
- Family identification → Family FASTA and map: writes FASTA and map
- OGGI CLI → Local synteny: dispatches subcoli
- Family FASTA and map → Local synteny: supplies family map
- Local synteny → Bioinformatics tools: searches with DIAMOND
- Local synteny → Collinearity algorithms: calls
- Local synteny → Collinear pairs: writes observed pairs
- OGGI CLI → Cluster engine: dispatches cluster
- Family FASTA and map → Cluster engine: supplies targets
- Collinear pairs → Cluster engine: supplies evidence
- Cluster engine → Bioinformatics tools: uses clustering tools
- Cluster engine → Partitions and reports: writes partitions and reports
- OGGI CLI → BUSCO assessment: dispatches busco
- BUSCO assessment → Bioinformatics tools: runs BUSCO
- BUSCO assessment → BUSCO results: writes results
- OGGI CLI → Species-tree inference: dispatches species-tree
- BUSCO results → Species-tree inference: supplies loci
- Species-tree inference → Bioinformatics tools: uses MAFFT and IQ-TREE
- Species-tree inference → Species tree: writes Newick
- OGGI CLI → Family HOG inference: dispatches hog-tree
- Family FASTA and map → Family HOG inference: supplies family sequences
- Species tree → Family HOG inference: supplies species tree
- Family HOG inference → HOG algorithms: calls
- Family HOG inference → Partitions and reports: writes HOG assignments
- OGGI CLI → Whole-proteome OrthoFinder: dispatches orthofinder
- Whole-proteome OrthoFinder → Bioinformatics tools: runs OrthoFinder
- OGGI CLI → OrthoFinder HOG import: dispatches HOG import
- Whole-proteome OrthoFinder → OrthoFinder HOG import: provides results
- OGGI CLI → Standalone wrappers: dispatches wrappers
- Standalone wrappers → Bioinformatics tools: runs selected tool