CorgiSNPs is a fungal core-genome SNP pipeline that can:
🧬 Detect SNPs from fungal whole-genome sequencing data
🧬 Handle organisms with up to 3 genome copies (haploid to triploid)
🧬 Generate phylogenies and pairwise distance matrices
🧬 Provide sample- and cluster-level summaries suitable for downstream visualization
🧬 Export results in standard formats (VCF, FASTA, Newick, CSV, Microreact)
CorgiSNPs is designed for public health fungal genomics (currently only tested with Candidozyma auris (Candida auris)). It builds on the foundation of MycoSNP but improves workflow automation, handling of higher ploidy organisms, and phylogenetic interpretation.
- Prepare – Prepare inputs (read QC, etc.,)
- Classify – De novo assembly, speciation, and subtyping
- Variants – Reference-based variant calling
- AMR – Detection of antifungal resistance markers
- Phylo – Core SNP phylogenetics and distance metrics
- Report – Interactive and static summaries
See the documentation for usage and setup details. (coming soon!)
samplesheet.csv:
sample,fastq_1,fastq_2
sample01,sample01_R1.fastq,sample01_R2.fastq
nextflow run DOH-JDJ0303/CorgiSNPs \
-r main \
-profile docker \
--input samplesheet.csv \
--outdir results/ \
--db db/ \
--push true
CorgiSNPs would not be possible without the contributions of:
- Washington State Department of Health – Public Health Laboratories
- Collaborators at CDC Mycotics Branch
- nf-core and the broader Nextflow community
CorgiSNPs was originally written by Jared Johnson for fungal pathogen surveillance at the Washington State Department of Health.