feat: added whole-genome reference comparison and variant annotation

.test/config/config.yml

@@ -50,3 +50,19 @@ synteny:
   extra: ""
   viz_scale: "1e6"
   viz_extra: "--normalize"
+
+reference_comparison:
+  skip: False
+  minimap2:
+    extra: "-c --cs"
+    sorting: "coordinate"
+    sort_extra: "--no-PG"
+  paftools:
+    extra: ""
+  bcftools:
+    extra: ""
+  snpeff:
+    build:
+      extra: "-noCheckCds -noCheckProtein -noLog -q"
+    annotate:
+      extra: "-nodownload -ud 0 -noLog"

README.md

@@ -30,15 +30,18 @@ _Workflow overview:_
 
 ## Workflow overview
 
-1. Parse `samples.csv` table containing the samples's meta data (`python`)
+1. Parse `samples.csv` table containing the samples's meta data (`python`).
 2. Annotate assemblies using one of the following tools:
-   1. NCBI's Prokaryotic Genome Annotation Pipeline ([PGAP](https://github.com/ncbi/pgap)). Note: needs to be installed manually
-   2. [prokka](https://github.com/tseemann/prokka), a fast and light-weight prokaryotic annotation tool
-   3. [bakta](https://github.com/oschwengers/bakta), a fast, alignment-free annotation tool. Note: Bakta will automatically download its companion database from zenodo (light: 1.5 GB, full: 40 GB)
-3. Predict antimicrobial resistance (AMR) genes using [RGI](https://github.com/arpcard/rgi)
-4. Create a QC report for the assemblies using [Quast](https://github.com/ablab/quast)
-5. Create a pangenome analysis (orthologs/homologs) using [Panaroo](https://gthlab.au/panaroo/)
+   1. NCBI's Prokaryotic Genome Annotation Pipeline ([PGAP](https://github.com/ncbi/pgap)). Note: needs to be installed manually.
+   2. [prokka](https://github.com/tseemann/prokka), a fast and light-weight prokaryotic annotation tool.
+   3. [bakta](https://github.com/oschwengers/bakta), a fast, alignment-free annotation tool. Note: Bakta will automatically download its companion database from zenodo (light: 1.5 GB, full: 40 GB).
+3. Predict antimicrobial resistance (AMR) genes using [RGI](https://github.com/arpcard/rgi).
+4. Create a QC report for the assemblies using [Quast](https://github.com/ablab/quast).
+5. Create a pangenome analysis (orthologs/homologs) using [Panaroo](https://gthlab.au/panaroo/).
 6. Compute pairwise average nucleotide identity (ANI) between the assemblies using [FastANI](https://github.com/ParBLiSS/FastANI) and plot a phylogenetic tree based on the ANI distances.
+7. Estimate genome completeness and contamination with [checkM2](https://github.com/chklovski/CheckM2).
+8. Detect and visualize multi-genome synteny with [ntSynt](https://github.com/BirolLab/ntSynt) and [ntSynt-viz](https://github.com/BirolLab/ntSynt-viz).
+9. Compute pairwise whole-genome reference comparison and annotate variant effects with [minimap2](https://github.com/lh3/minimap2), [vcftools](https://github.com/vcftools/vcftools), [bcftools](https://github.com/samtools/bcftools) and [snpEff](https://github.com/pcingola/snpeff).
 
 ## Installation
 
@@ -119,6 +122,6 @@ snakemake --cores 2 --sdm conda apptainer --directory .test
 
 > Köster J., Mölder F., Jablonski K. P., Letcher B., Hall M. B., Tomkins-Tinch C. H., Sochat V., Forster J., Lee S., Twardziok S. O., Kanitz A., Wilm A., Holtgrewe M., Rahmann S., & Nahnsen S. _Sustainable data analysis with Snakemake_. F1000Research, 10:33, 10, 33, **2021**. https://doi.org/10.12688/f1000research.29032.2.
 
-> Coombe L, Kazemi P, Wong J, Birol I, Warren RL. _ntSynt: multi-genome synteny detection using minimizer graph mappings_. BMC Biology. 23:367, **2025**. https://doi.org/10.1186/s12915-025-02455-w
+> Coombe L, Kazemi P, Wong J, Birol I, Warren RL. _ntSynt: multi-genome synteny detection using minimizer graph mappings_. BMC Biology., 23:367, **2025**. https://doi.org/10.1186/s12915-025-02455-w
 
-> Coombe L, Warren RL, Birol I. _ntSynt-viz: Visualizing synteny patterns across multiple genomes_. bioRxiv 2025.01.15.633221. https://doi.org/10.1101/2025.01.15.633221
+> Coombe L, Warren RL, Birol I. _ntSynt-viz: Visualizing synteny patterns across multiple genomes_. J. Evol. Biol., **2026**. https://doi.org/10.1093/jeb/voag079

config/config.yml

@@ -50,3 +50,19 @@ synteny:
   extra: ""
   viz_scale: "1e6"
   viz_extra: "--normalize"
+
+reference_comparison:
+  skip: False
+  minimap2:
+    extra: "-c --cs"
+    sorting: "coordinate"
+    sort_extra: "--no-PG"
+  paftools:
+    extra: ""
+  bcftools:
+    extra: ""
+  snpeff:
+    build:
+      extra: "-noCheckCds -noCheckProtein -noLog -q"
+    annotate:
+      extra: "-nodownload -ud 0 -noLog"

config/schemas/config.schema.yml

@@ -200,6 +200,74 @@ properties:
       - extra
       - viz_extra
       - viz_scale
+  reference_comparison:
+    type: object
+    properties:
+      skip:
+        type: boolean
+        description: Whether to skip whole-genome reference comparison
+        default: false
+      minimap2:
+        type: object
+        properties:
+          extra:
+            type: string
+            description: Extra command-line arguments for minimap2 analysis
+            default: "-c --cs"
+          sorting:
+            type: string
+            description: Sorting method for minimap2 output (e.g., "coordinate" or "queryname")
+            default: "coordinate"
+          sort_extra:
+            type: string
+            description: Extra command-line arguments for sorting minimap2 output
+            default: "--no-PG"
+        required:
+          - extra
+          - sorting
+          - sort_extra
+      paftools:
+        type: object
+        properties:
+          extra:
+            type: string
+            description: Extra command-line arguments for paftools analysis
+            default: ""
+        required:
+          - extra
+      bcftools:
+        type: object
+        properties:
+          extra:
+            type: string
+            description: Extra command-line arguments for bcftools analysis
+            default: ""
+        required:
+          - extra
+      snpeff:
+        type: object
+        properties:
+          build:
+            type: object
+            properties:
+              extra:
+                type: string
+                description: Extra command-line arguments for snpEff build
+                default: "-noCheckCds -noCheckProtein -noLog -q"
+            required:
+              - extra
+          annotate:
+            type: object
+            properties:
+              extra:
+                type: string
+                description: Extra command-line arguments for snpEff annotate
+                default: "-nodownload -ud 0 -noLog"
+            required:
+              - extra
+        required:
+          - build
+          - annotate
 required:
   - samplesheet
   - tool
@@ -213,3 +281,4 @@ required:
   - checkm
   - rgi
   - synteny
+  - reference_comparison