bio-comparative-genomics-pangenome-analysis

## Version Compatibility Reference examples tested with: Panaroo 1.5.1+ (Tonkin-Hill 2020 Genome Biol 21:180), PPanGGOLiN 2.2.0+ (Gautreau 2020 PLoS Comp Biol 16:e1007732), PEPPAN 1.0.5+ (Zhou 2020 GR 30:1667), GET_HOMOLOGUES 25102023+, anvi'o 8.0+ (Eren 2021 Nat Microbiol 6:3), Minigraph-Cactus (Hickey 2024 Nat Biotech 42:663; bundled with Cactus 2.5+), PGGB 0.7.5+ (Garrison 2024 Nat Methods 21:2008), vg 1.59.0+ (Sirén J et al 2024 Nat Methods 21:2017), PanGenie 3.1.0+ (Ebler 2022 Nat Genet 54:518), PGR-TK 0.3.6+ (Chin 2023 Nat Methods 20:1213; cschin/pgr-tk; repo archived April 2026 transitioning to PANGEA), PANGEA (in development by DGI / Diploid Genomics as PGR-TK's successor for pangenome graph exploration + analysis -- check https://github.com/cschin/pgr-tk for current repository pointer), Bakta 1.10.4+ (annotation for input), Roary 3.13.0+ (DEPRECATED; use Panaroo), Scoary 1.6.16+, pyseer 1.3.11+, BUSCO 5.7+, FastTree 2.1.11+, RAxML-NG 1.2+. Python 3.10+ required for Panaroo / PPanGGOLiN. Before using code patterns, verify installed versions match. If versions differ: - CLI: `panaroo --version`; `ppanggolin --version`; `peppan --help`; `cactus-pangenome --help`; `pggb --version`; `vg version` - Python: `pip show panaroo ppanggolin` If code throws `Bakta annotation incompatible`, `GFA file inconsistent`, `vg index version mismatch`, the bacterial pangenome ecosystem expects consistent annotation; re-annotate all input genomes with the same tool and version before pangenome analysis. # Pangenome Analysis **"What genes are universal vs accessory across this set of genomes?"** -> The pangenome is the union of all genes across a sampled group; the **Tettelin partition** (Tettelin 2005 PNAS 102:13950) splits it into core (universal), shell (in many but not all), cloud (rare), and species-specific (private) genes. The fundamental dichotomy is **bacterial pangenome** (clusters genes into orthogroups; Panaroo / PPanGGOLiN / PEPPAN for compact genomes) vs **eukaryotic pangenome** (graph-based; Minigraph-Cactus / PGGB / vg for haplotype-resolved sequences). The choice depends on what's being represented: bacterial pangenome captures gene-content variation in a species/genus; eukaryotic pangenome graph captures haplotype-level structural and sequence variation. **Roary (Page 2015) is now deprecated** in favor of Panaroo, which handles annotation-error noise that previously inflated bacterial pangenomes substantially. - CLI: `panaroo -i annotated_gffs/ -o panaroo_out --clean-mode strict --remove-invalid-genes` -- bacterial pangenome - CLI: `ppanggolin workflow --fasta fasta_list.tsv --output ppanggolin_out` -- partitioned bacterial pangenome - CLI: `peppan -i genomes.gff -o peppan_out` -- genus-scale bacterial pangenome - CLI: `cactus-pangenome jobStore seqFile.txt --reference name --vcf --gfa` -- Minigraph-Cactus pangenome - CLI: `pggb -i genomes.fa.gz -n 90 -t 32 -o pggb_out` -- PGGB pangenome graph - CLI: `vg autoindex --workflow giraffe -r ref.fa -v variants.vcf.gz` -- vg pangenome indexing ## Algorithmic Taxonomy | Tool | Approach | Output | Strength | Fails when | |------|----------|--------|----------|------------| | Panaroo (Tonkin-Hill 2020 GB 21:180) | Graph-based ortholog clustering + annotation-error correction | Core, shell, accessory pangenome with cleaned annotations | Best for clonal bacteria (Mtb 413-genome benchmark; Tonkin-Hill 2020) | Slow for > 10000 genomes; assumes Prokka/Bakta input | | PPanGGOLiN (Gautreau 2020 PLoS CB 16:e1007732) | Hidden Markov partition: persistent/shell/cloud | Partitioned pangenome with HMM-based class assignment | Scales to many genomes; interpretable partitions | Probabilistic class boundaries differ from strict Tettelin | | PEPPAN (Zhou 2020 GR 30:1667) | Bacterial pangenome for diverse genera | Pan + core genomes from 1000s of genomes | Designed for high diversity (whole genus) | Slower than newer alternatives at small scales | | Roary (Page 2015; DEPRECATED) | Original bacterial pangenome | Same outputs as Panaroo | Legacy; widely cited | Inflates accessory substantially due to annotation-error tolerance; use Panaroo | | GET_HOMOLOGUES (Contreras-Moreira 2013) | Multi-algorithm consensus (OrthoMCL, BDBH, COG) | Consensus pangenome | Cross-validates across methods | Slower; multi-program output integration | | anvi'o pangenomics (Eren 2021 Nat Microbiol 6:3) | Interactive pangenome with metadata | Visual pangenome browsing + integration | Standard for interactive microbial pangenome | Less automated; manual curation expected | | Minigraph-Cactus (Hickey 2024 Nat Biotech 42:663) | Cactus base-level + minigraph SV-graph integration | Pangenome graph (GFA, VCF, GBZ) | Production-grade for HPRC-scale haplotypes | Requires reference; designed for intra-species pangenome | | PGGB (Garrison 2024 Nat Methods 21:2008) | All-vs-all wfmash + seqwish | Pangenome graph (GFA) | Modern reference-free graph; HPRC-validated | Computationally heavy at > 100 genomes | | vg pangenome (Sirén J et al 2024 Nat Methods 21:2017) | Pangenome graph indexing + Giraffe / GiraffeY mapping | Mapped reads to graph + variant calling | vg ecosystem standard for graph-based variant calling | Setup complex; learning curve | | PanGenie (Ebler 2022 Nat Genet 54:518) | Pangenome-graph-based genotyping | SV genotype calls | Efficient genotyping from short reads via graph | Requires pre-built pangenome graph | | PGR-TK (Chin 2023 Nat Methods 20:1213; cschin/pgr-tk) | Minimizer Anchored Pangenome (MAP) graph + principal bundle decomposition | Multiscale pangenome graph; bundle SVGs; AGC-backed sequence db | Designed for repetitive / clinically-relevant genes (MHC class II, DAZ1-4, OPN1LW/OPN1MW); decomposes tangled graph into interpretable bundles; complements Minigraph-Cactus by exposing fine-grained allele structure | Repo archived April 2026 -> PANGEA succession; pinned to Peregrine-assembler-derived workflow; not a drop-in for variant-calling pipelines | | PANGEA (in development by DGI / Diploid Genomics; succeeds PGR-TK; check cschin/pgr-tk for current pointer) | Next-generation MAP-graph framework | Same conceptual outputs as PGR-TK with modernized API | Active development 2026+; expected to add tighter integration with HPRC / T2T workflows | API surface in flux; pin specific version when scripting | | Heaps law / Tettelin (Tettelin 2005 PNAS 102:13950) | Statistical model of pangenome openness | Open / closed pangenome classification | Foundational framework | Class boundaries depend on sampling | | Scoary (Brynildsrud 2016) | Pan-GWAS on gene presence/absence | Phenotype-gene associations | Standard bacterial pan-GWAS tool | Limited to binary phenotypes | | pyseer (Lees 2018 Bioinformatics 34:4310) | Continuous + binary phenotype association on k-mers/genes | Pan-GWAS with k-mer / gene-content units | More flexible than Scoary | Computational cost | | pirate (Bayliss 2019) | Bacterial pangenome from multiple methods | Cross-method consensus | Alternative to GET_HOMOLOGUES | Less popular now | Methodology evolves; verify the current Panaroo and PPanGGOLiN manuals + the 2024-2025 microbial pangenome reviews. The HPRC draft pangenome (Liao 2023 Nature 617:312) sets the modern eukaryotic pangenome standard; for bacterial work, Panaroo + PPanGGOLiN is the standard combination. ## Decision Tree by Experimental Scenario | Scenario | Recommended approach | Why | |----------|------------------------|-----| | Bacterial strain set (5-1000 genomes) of one species | Panaroo + PPanGGOLiN | Cross-validation; Panaroo's annotation-cleaning + PPanGGOLiN's partition | | Bacterial genus-level pangenome (> 1000 genomes) | PEPPAN | Designed for high genus-level diversity | | Mycobacterium tuberculosis (clonal) | Panaroo | Tonkin-Hill 2020 benchmark; clonal pangenomes | | E. coli (highly diverse) | PPanGGOLiN or PEPPAN | High accessory diversity | | Eukaryotic intra-species pangenome (e.g. human, soybean) | Minigraph-Cactus or PGGB | Graph-based; SV-aware | | HPRC-style 90 haplotype graph | Minigraph-Cactus | Production-grade for HPRC scale | | Reference-free eukaryotic pangenome | PGGB | All-vs-all alignment-free graph | | Pangenome graph for variant calling | vg autoindex -> vg giraffe | Standard graph-aligner ecosystem | | Bacterial pan-GWAS for phenotype | Panaroo + Scoary or pyseer | Pangene matrix from Panaroo; pan-GWAS tool | | Visualize pangenome interactively | anvi'o pangenomics workflow | Standard for interactive analysis | | Distinguish core / shell / cloud genes | PPanGGOLiN (HMM-partitioned) or Tettelin manual partition on Panaroo output | Standard Tettelin framework | | Open vs closed pangenome (Heaps law) | wgd v2 statistical fit OR custom mclust on Panaroo output | Tettelin 2005 framework | | Detect HGT-acquired accessory genes | Cross-reference with [[hgt-detection]] | Pangenome + phylogeny | | Eukaryotic structural-variation indexing | Minigraph-Cactus -> vg + PanGenie | SV-aware genotyping pipeline | | Bacterial functional pangenome | Panaroo + eggNOG-mapper + KEGG | Functional annotation | | Pangenome-aware reference for read alignment | vg giraffe with pangenome graph | Reduces reference bias | | Genome-graph-based fine-mapping | vg + GraphAligner or vg giraffe | SV-aware short-read alignment | | Repetitive / clinically relevant gene (MHC class II, DAZ1-4, OPN1LW/OPN1MW) | PGR-TK MAP graph + principal bundle decomposition | Built for tangled repeat graphs; bundle decomposition reveals haplotype-allele structure that linear refs collapse | | Next-gen pangenome graph exploration (2026+) | PANGEA (PGR-TK successor, in development by DGI / Diploid Genomics) | Modernized successor to PGR-TK; check cschin/pgr-tk pointer for current repo | | HLA / KIR / immune-locus pangenome | PGR-TK + manual bundle inspection | Standard tools collapse repeat alleles; PGR-TK's bundle decomposition preserves them | ## Per-Tool Failure Modes ### Annotation heterogeneity inflating accessory genome **Trigger:** Running Panaroo on Prokka- vs Bakta- vs RefSeq- annotated genomes mixed. **Mechanism:** Different annotation tools predict different gene boundaries; the same gene is annotated slightly differently across tools, appearing as separate orthogroups. Roary's tolerance of these differences inflated the bacterial accessory genome substantially -- nearly an order of magnitude on the clonal M. tuberculosis benchmark (Tonkin-Hill 2020 GB 21:180). Panaroo's graph-based correction reduces this but cannot eliminate it. **Symptom:** Per-strain "accessory" gene count is inflated relative to known biology; comparison to a single-pipeline reference reveals substantial spurious gene-content differences. **Fix:** Re-annotate ALL genomes with one pipeline (currently Bakta 1.10.4+ for bacteria; Bakta is GenBank-compliant and faster than Prokka). Use `panaroo --clean-mode strict --remove-invalid-genes` to apply graph cleaning. Document annotation pipeline + version in methods. ### Tettelin partition class boundary artifacts **Trigger:** Reporting "core genome" vs "accessory" as percent-of-strains thresholds (e.g. 99% = core). **Mechanism:** Tettelin 2005 used 100%-presence = core; pragmatic studies use 95%-99%. The class boundary is arbitrary; small variation in the threshold dramatically changes core/accessory ratio. **Symptom:** Core genome size varies 10-30% depending on whether threshold is 95% or 99%. **Fix:** Report core/shell/cloud at multiple thresholds; PPanGGOLiN's HMM partition is more principled but still has tunable parameters. Standard reporting: core = present in >=95% (or >=99%); shell = 15-95%; cloud = < 15%. Document threshold. ### Roary's annotation-error noise (DEPRECATED tool) **Trigger:** Using Roary in new analyses. **Mechanism:** Roary tolerates annotation errors (low-identity matches; protein-vs-DNA matches), producing thousands of artifactual accessory genes. Panaroo's introduction (Tonkin-Hill 2020) demonstrated this by re-analyzing 413 Mtb genomes and finding Panaroo's accessory genome was nearly an order of magnitude smaller than the inflated tools' (Roary included). **Symptom:** Roary output has many "lineage-specific genes" with poor evidence (single-strain hits, short proteins, no functional annotation). **Fix:** Migrate to Panaroo. Panaroo can read Roary's input format; for legacy projects, re-run with Panaroo and compare. Panaroo's `--clean-mode strict` enforces strict graph-based quality control. ### Pangenome graph reference bias (eukaryote) **Trigger:** Using Minigraph-Cactus with a single reference; calling variants against the "reference" path. **Mechanism:** Minigraph-Cactus is reference-anchored; the chosen reference appears throughout the graph as a privileged path. Variants are called relative to the reference path; non-reference haplotypes are under-represented in the variant calling. **Symptom:** Variant call density on non-reference haplotypes is lower than on reference; allele frequencies skewed toward reference. **Fix:** Use PGGB (reference-free) for less reference-biased analysis. Alternatively, treat the reference choice as a methodological parameter and document. For HPRC, multiple references can be used and results pooled. ### Heaps law misapplied **Trigger:** Concluding "open pangenome" from a single Heaps-law fit on insufficient data. **Mechanism:** Heaps law parameter alpha distinguishes open (alpha < 1) from closed (alpha > 1) pangenome; estimation requires sampling many genomes. Few genomes give unstable estimates. **Symptom:** Heaps-law alpha varies by > 0.2 across resampling; conclusions about pangenome openness flip. **Fix:** Require >= 50 genomes (preferably > 100) for Heaps-law estimation; report 95% CI from resampling. Tettelin 2005 demonstrated open Streptococcus agalactiae; Vernikos 2015 reviews open vs closed across taxa. ### PGGB memory exhaustion at many genomes **Trigger:** Running PGGB with > 30 large eukaryotic genomes on a single node. **Mechanism:** PGGB's wfmash all-vs-all step has O(N^2) memory pattern; large eukaryotic genomes (> 1 Gb) make memory prohibitive for > 30 input genomes. **Symptom:** PGGB OOMs at the wfmash stage; cluster job killed by OOM-killer. **Fix:** Use Minigraph-Cactus for > 30 genomes (it scales better); or split PGGB into chromosomes/regions. PGGB recommendation is <= 20 large genomes per run. ### vg index version mismatch breaking giraffe **Trigger:** Pre-built vg index used with a different vg version for read alignment. **Mechanism:** vg index format evolved; pre-built indexes from one version may not be compatible with another. **Symptom:** vg giraffe fails with "index version" error. **Fix:** Rebuild vg index with current version; or pin vg version for an analysis. Future vg releases promise backward compatibility but verify. ### PanGenie genotype false positives in repetitive regions **Trigger:** PanGenie on highly repetitive regions (centromeres, segmental duplications). **Mechanism:** Pangenome-graph-based genotyping requires unique paths in the graph; highly repetitive regions create graph-spaghetti paths that are difficult to genotype reliably. **Symptom:** PanGenie calls many heterozygous SVs in known-repetitive regions; quality scores low. **Fix:** Restrict PanGenie to non-repetitive regions; combine with traditional read-based SV callers (DELLY, Manta) for repeat regions. The HPRC paper documents this limitation (Liao 2023). ### Bacterial pangenome with frequent gene-content recombination **Trigger:** Building a pangenome of a species with extensive recombination (e.g. Neisseria, Streptococcus pneumoniae). **Mechanism:** Frequent recombination breaks the "vertical inheritance" assumption underlying ortholog clustering; the same gene appears in many phylogenetic positions across strains, complicating orthology and inflating accessory genome. **Symptom:** Phylogenetic trees from core genome are unstable; per-gene trees show extensive incongruence; pangenome accessory genome appears artificially large. **Fix:** Use ClonalFrameML (Didelot 2015 PLoS Comp Biol 11:e1004041) to identify recombinant regions; mask them before pangenome analysis. Restrict core genome analysis to non-recombinant regions. ### Annotation density variation across genomes **Trigger:** Mixing well-annotated reference genomes with newly assembled, draft-annotation genomes. **Mechanism:** Draft annotations miss small genes, pseudogenes, and lineage-specific genes; well-annotated genomes have these. Comparing them inflates "accessory" in draft genomes. **Symptom:** Draft genomes have 200-500 fewer accessory genes than expected; per-genome BUSCO completeness > annotation completeness. **Fix:** Re-annotate all genomes consistently with Bakta + Prodigal; document BUSCO completeness for each. Exclude genomes with > 5% lower BUSCO than median. ## Quantitative Thresholds | Quantity | Threshold | Source / Rationale | |----------|-----------|-------------------| | Core genome threshold | >=95% (relaxed) to 100% (strict) of strains | Tettelin 2005; pragmatic | | Shell genome | 15-95% (or 5-95% per PPanGGOLiN) | PPanGGOLiN docs | | Cloud genome | < 15% of strains | Tettelin 2005 | | Heaps law alpha (open) | < 1 | Tettelin 2005 | | Heaps law alpha (closed) | > 1 | Tettelin 2005 | | Minimum genomes for Heaps law fit | >= 50; >= 100 preferred | Vernikos 2015 | | Panaroo gene cluster identity | >=70% (default); stricter for clonal | Panaroo defaults | | PPanGGOLiN coverage | 80% gene-length coverage in clustering | Default | | PEPPAN BLAT threshold | identity >= 70% | Zhou 2020 | | Mycobacterium tuberculosis core | ~3500-3700 genes (Tonkin-Hill 2020 Mtb benchmark) | Bench results | | E. coli pangenome (open) | core ~2400; pangenome >15000 | Reference | | Plasmodium falciparum core | ~5300 genes (eukaryotic prokaryote-like) | Reference | | Minimum strains for bacterial pangenome | >= 5; >= 20 for shell/cloud meaningful | Empirical | | HPRC pangenome size | 90 haplotypes, ~6.4M variants | Liao 2023 | | PGGB recommended max genomes | <= 20 large eukaryotic; 100+ for compact | Garrison 2024 | | PanGenie minimum k-mer | k = 31 default | Ebler 2022 | | vg index Haplotype Sampling | --haplotype-sampling YES for multi-pop graph | Sirén J et al 2024 Nat Methods 21:2017 | | Scoary pan-GWAS p-value threshold | Bonferroni-corrected p < 0.05 | Brynildsrud 2016 | | pyseer continuous-trait power | requires > 1000 isolates for solid signal | Lees 2018 | | anvi'o pangenome minimum | 5+ genomes for non-trivial visualization | Eren 2021 | ## Panaroo Bacterial Pangenome Workflow **Goal:** Construct a high-quality bacterial pangenome with annotation-error correction. **Approach:** Annotate genomes consistently with Bakta -> run Panaroo strict mode -> partition with PPanGGOLiN. ```bash # 1. Annotate all genomes with Bakta (consistent annotation) mkdir -p annotated for fa in genomes/*.fa; do name=$(basename $fa .fa) bakta --db /path/to/bakta-db --threads 16 \ --output annotated/${name} --prefix $name \ --genus Escherichia --species coli \ $fa done # 2. Run Panaroo panaroo -i annotated/*.gff -o panaroo_out -t 16 \ --clean-mode strict --remove-invalid-genes # 3. Extract pangenome matrix # panaroo_out/gene_presence_absence.csv strains x genes matrix # panaroo_out/core_gene_alignment.aln core gene MSA for phylogeny # panaroo_out/pan_genome_reference.fa consensus pangenome sequence # 4. Tettelin partition (custom) python tettelin_partition.py \