Part of the rMAP-suite

rMAP-GWAS

Reproducible microbial genome-wide association workflow for case–control and phenotype–genotype discovery, with gene presence/absence GWAS, optional SNP GWAS, and Gubbins recombination assessment.

Launch example reports View workflow architecture GitHub repository
Association modesGene + SNP
Structure correctionMash + pyseer
RecombinationOptional Gubbins

Launch rMAP-GWAS reports

Open the interactive example reports generated by the workflow. These cards point to the GitHub Pages report paths under docs/reports/.

MTBC MRSA/MSSA CRAB/CSAB blaOXA-23 VRE/VSE blaKPC rpoB SNP Gene GWAS SNP GWAS Gubbins Test run
Mycobacterium tuberculosis complex dataset docs/reports/MTBC_rpoB

rpoB marker-positive versus marker-negative

Positive-control MTBC SNP-GWAS report contrasting rpoB 763031 T→C marker-present and marker-absent isolates, with the expected Rv0667/rpoB signal recovered and annotated.

Cases50 marker-positive
Controls50 marker-negative
Total100 samples
rpoB 763031 hit MTBC reference SNP GWAS
Open interactive report →
Klebsiella pneumoniae dataset docs/reports/blaKPC

blaKPC-positive versus blaKPC-negative

Positive-control K. pneumoniae AMR GWAS report contrasting blaKPC-positive and blaKPC-negative isolates, with the expected blaKPC gene signal recovered, SNP GWAS enabled, and Gubbins recombination assessment run.

Cases50 blaKPC+
Controls50 blaKPC−
Total100 samples
blaKPC signal K. pneumoniae Gubbins run
Open interactive report →
Staphylococcus aureus dataset docs/reports/Staphylococcus_aureus

MRSA versus MSSA

Positive-control S. aureus GWAS report contrasting methicillin-resistant and methicillin-susceptible isolates, with gene presence/absence association testing and MRSA-enriched marker review.

Cases50 MRSA
Controls50 MSSA
Total100 samples
mecA signal S. aureus pyseer
Open interactive report→
Acinetobacter baumannii dataset docs/reports/Acinetobacter_baumannii_CRAB_OXA23

CRAB versus CSAB

Positive-control A. baumannii AMR GWAS report contrasting carbapenem-resistant, OXA-23-positive isolates with carbapenem-susceptible, OXA-23-negative isolates, with gene presence/absence association testing, population-structure assessment, and prioritized marker review.

Cases50 CRAB
Controls50 CSAB
Total100 samples
blaOXA-23 signal A. baumannii Gene GWAS
Open interactive report →
Enterococcus faecium dataset docs/reports/Enterococcus_faecium

VRE versus VSE

Positive-control E. faecium AMR GWAS report contrasting vancomycin-resistant and vancomycin-sensitive isolates, with gene presence/absence association testing, population-structure visualization, and ranked candidate marker review.

Cases50 VRE
Controls50 VSE
Total100 samples
vancomycin AMR E. faecium group_574 hit
Open interactive report→
Local test dataset docs/reports/test

Four-sample MRSA versus MSSA test

Lightweight smoke-test report using four downsampled S. aureus paired-end samples. The run checks local/Terra-ready execution, gene GWAS, optional SNP-GWAS output rendering, and report generation.

Cases2 MRSA
Controls2 MSSA
Total4 samples
test run Gene GWAS SNP GWAS
Launch test report→

Workflow architecture

The workflow follows a five-stage architecture covering study design and QC, assembly and annotation, pangenome/population structure, association testing, and interactive reporting.

01

Study design & read QC

  • Paired-end FASTQ inputs
  • Case/control phenotype table
  • fastp trimming and QC summaries
02

Assembly & annotation

  • Shovill de novo assembly
  • QUAST assembly QC
  • Prokka/Bakta-compatible annotation outputs
03

Pangenome & structure

  • Panaroo gene presence/absence matrix
  • Mash pairwise distances
  • PCoA and heatmap interpretation aids
04

GWAS association testing

  • pyseer gene presence/absence GWAS
  • Optional SNP marker GWAS
  • Effect size, p-value, and q-value summaries
05

Visualization & reporting

  • Interactive HTML report
  • QQ and Manhattan-style plots
  • Prioritized hits and annotation rescue

Gubbins recombination module

The workflow includes an optional Gubbins branch for recombination-aware SNP interpretation.

How to interpret this module: Gubbins is used as an optional recombination assessment branch after core/SNP alignment generation. It helps distinguish vertically inherited SNP signal from potentially recombinant regions before interpreting SNP GWAS and phylogenetic structure.
InputCore/SNP alignmentAlignment generated from selected samples and reference-guided SNP calling.
FilterGubbinsDetects recombination blocks and creates recombination-aware outputs.
ReportInterpretationSummaries are surfaced next to SNP GWAS and phylogeny outputs.
Optional SNP GWAS branch
  ├─ Snippy/reference-guided SNP calling
  ├─ Core/SNP alignment
  ├─ Gubbins recombination assessment
  ├─ pyseer SNP association testing
  └─ Integrated HTML report outputs

Key report caution:
  Recombination, lineage structure, small cohorts,
  PE/PPE genes, and repetitive regions require manual review.