rMAP-Candida (Rapid Mycological Analysis Pipeline)

rMAP-Candida is a reproducible, Dockerized WDL/Cromwell workflow for public-health-oriented whole-genome sequencing analysis of Candida species. The workflow supports paired-end Illumina FASTQ inputs and integrates read preprocessing, sequence quality control, species typing, genome assembly, assembly-quality assessment, antifungal-resistance marker screening, phylogenomic analysis & integrated HTML report generation.

rMAP-Candida was developed to support genomic surveillance of clinically important Candida spp. by combining standardized quality control, species identification, genome assembly, resistance-marker interpretation & surveillance-ready reporting within a portable & reproducible workflow framework. It is designed for local workstation, server, HPC & cloud-compatible execution using Docker containers & Cromwell/WDL workflow orchestration.

The workflow begins with paired-end FASTQ validation, read preprocessing, FastQC-based sequence quality assessment & MultiQC aggregation. It then performs Candida species typing, genome assembly, assembly-quality summarization & downstream interpretation of genomic features relevant to antifungal resistance & fungal genomic surveillance.

rMAP-Candida is designed to support analysis of major clinically relevant Candida species, including Candida albicans, Candida auris, Candida parapsilosis, Candida tropicalis, Candida glabrata & Candida krusei. The workflow provides structured outputs that can support research, outbreak preparedness, antimicrobial-resistance surveillance & implementation of fungal genomics in public health laboratories.

For antifungal-resistance surveillance, rMAP-Candida supports conservative screening & reporting of resistance-associated markers & genes such as ERG11, FKS1, FKS2, MDR1 & CDR1, depending on the species & available reference resources. These outputs are intended to support surveillance & research interpretation rather than replace clinical antifungal susceptibility testing.

rMAP-Candida generates integrated HTML reports & downloadable surveillance outputs, including QC summaries, species-typing results, genome assembly metrics, antifungal-resistance marker summaries, phylogenomic outputs & interpretable tables suitable for review by bioinformaticians, microbiologists, public health teams & collaborating investigators.

Key workflow capabilities include:

• Read quality control & preprocessing — validates paired-end FASTQ inputs, performs read-level quality assessment & summarizes sequencing quality using standardized QC outputs.
• Candida species typing — identifies and summarizes clinically relevant Candida species to support fungal genomic surveillance & dataset interpretation.
• Genome assembly and assembly-quality assessment — assembles fungal genomes and reports interpretable assembly metrics such as genome size, contiguity & quality indicators.
• Antifungal-resistance marker screening — summarizes known or putative resistance-associated markers in key genes relevant to azole & echinocandin resistance surveillance.
• Phylogenomic & comparative outputs — supports surveillance-oriented comparison of isolates through tree & relatedness outputs where appropriate.
• Integrated report generation — produces GitHub Pages-compatible HTML reports with downloadable outputs for QC, species typing, assembly metrics, resistance-marker summaries & surveillance interpretation.
• Reproducible workflow execution — uses Dockerized tools and WDL/Cromwell orchestration to support consistent execution across laptops, servers, HPC systems & cloud-compatible environments such as Terra.

The rMAP-Candida GitHub repository, documentation, workflow files, example inputs, and GitHub Pages-compatible reports are available here:
https://github.com/gmboowa/rMAP-Candida

The GitHub Pages report site is available here:
https://gmboowa.github.io/rMAP-Candida/