rMAP-Myc-Candida surveillance report

Integrated Candida fungal genomics report

This report summarizes paired-end fungal genome analysis for Candida-focused surveillance, combining read QC, Kraken2/Bracken species typing, MEGAHIT assembly, QUAST-only assembly contiguity assessment, and genomic antifungal-resistance screening.

Run generated: 2026-05-31 15:41:21 UTCRun stamp: 20260531_154121_UTCCustom Candida Kraken2/Bracken DBMEGAHIT assembly
Samples analyzed6
Top species groups1
Total AMR hits2
Median N50107,528

1. Executive summary

The primary detected fungal species group was Candida parapsilosis. The sample-level cards below provide a compact interpretation of species assignment, QUAST assembly-contiguity metrics, phylogeny status, and genomic AMR screening status.

Interpretation note: genomic antifungal-resistance findings should be treated as screening evidence. Clinically important results should be interpreted with isolate metadata, species identity, validated mutation catalogues, and phenotypic antifungal susceptibility testing where required.

Species distribution

Candida parapsilosis
6

2. Surveillance readiness and interpretation dashboard

This integrated table combines species confidence, QUAST assembly-contiguity metrics, AMR marker status, phylogeny eligibility, and optional metadata into a practical surveillance-readiness view.

SampleCollection datesitespeciesSpecies confidenceAssembly QCQUAST contiguity QCAMR screenPhylogenySurveillance statusReason / note
SRR283957272005Free StateCandida parapsilosisHighPassPassNo curated marker detectedExcludedReady for surveillance interpretationNo major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status
SRR283957282001GautengCandida parapsilosisHighPassPass1 marker(s)ExcludedReviewAMR marker detected
SRR283957322003GautengCandida parapsilosisHighPassPass1 marker(s)ExcludedReviewAMR marker detected
SRR283957382003Free StateCandida parapsilosisHighPassPassNo curated marker detectedExcludedReady for surveillance interpretationNo major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status
SRR283957392003Free StateCandida parapsilosisHighPassPassNo curated marker detectedExcludedReady for surveillance interpretationNo major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status
SRR283957402003Free StateCandida parapsilosisHighPassPassNo curated marker detectedExcludedReady for surveillance interpretationNo major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status

3. Surveillance metadata

Samplecountrysitecollection_datespecimen_typepatient_groupward_or_facilitysequencing_platform
SRR28395728South AfricaGauteng2001bloodhumanGautengILLUMINA; Illumina NovaSeq 6000
SRR30284754South AfricaSouth Africa2022-04-21bloodhumanSouth AfricaILLUMINA; NextSeq 2000
SRR28395739South AfricaFree State2003bloodhumanFree StateILLUMINA; Illumina NovaSeq 6000
SRR30284753South AfricaSouth Africa2022-04-21bloodhumanSouth AfricaILLUMINA; NextSeq 2000
SRR30284762South AfricaSouth Africa2022-03-01bloodhumanSouth AfricaILLUMINA; NextSeq 2000
SRR28395727South AfricaFree State2005bloodhumanFree StateILLUMINA; Illumina NovaSeq 6000
SRR28395732South AfricaGauteng2003bloodhumanGautengILLUMINA; Illumina NovaSeq 6000
SRR28395738South AfricaFree State2003bloodhumanFree StateILLUMINA; Illumina NovaSeq 6000
SRR28395740South AfricaFree State2003bloodhumanFree StateILLUMINA; Illumina NovaSeq 6000
SRR30284744South AfricaSouth Africa2023-05-16bloodhumanSouth AfricaILLUMINA; NextSeq 2000
SRR30284758South AfricaSouth Africa2022-04-11bloodhumanSouth AfricaILLUMINA; NextSeq 2000

4. Sample-level surveillance summary

SRR28395727

Candida parapsilosis Ready for surveillance interpretation
Species reads99.98%
Contigs396
N50112,532
GC (%)38.65

No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Excluded

Interpretation: No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.

SRR28395728

Candida parapsilosis Review
Species reads100.00%
Contigs404
N50105,599
GC (%)38.66

1 AMR hit(s) Species confidence: High Phylogeny: Excluded

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.

SRR28395732

Candida parapsilosis Review
Species reads100.00%
Contigs403
N50103,078
GC (%)38.64

1 AMR hit(s) Species confidence: High Phylogeny: Excluded

Interpretation: AMR marker detected. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.

SRR28395738

Candida parapsilosis Ready for surveillance interpretation
Species reads100.00%
Contigs449
N5085,376
GC (%)38.64

No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Excluded

Interpretation: No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.

SRR28395739

Candida parapsilosis Ready for surveillance interpretation
Species reads100.00%
Contigs408
N50110,836
GC (%)38.65

No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Excluded

Interpretation: No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.

SRR28395740

Candida parapsilosis Ready for surveillance interpretation
Species reads99.97%
Contigs406
N50109,456
GC (%)38.65

No curated genomic AMR marker detected — not susceptible Species confidence: High Phylogeny: Excluded

Interpretation: No major automated warning flags using species typing, QUAST assembly QC, AMR screening, and phylogeny status. Species note: Top species abundance ≥95%. Phylogeny note: Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.

5. Candida species typing using Kraken2/Bracken

Top species calls are derived from the custom Candida-focused Kraken2/Bracken database bundled in the species-typing Docker image.

SampleTop speciesReads (%)clade_readstaxon_readstaxidevidence
SRR28395727Candida parapsilosis
99.98%		5,351,1165,351,1165480Bracken species-level abundance
SRR28395728Candida parapsilosis
100.00%		6,435,8006,435,8005480Bracken species-level abundance
SRR28395732Candida parapsilosis
100.00%		4,494,1684,494,1685480Bracken species-level abundance
SRR28395738Candida parapsilosis
100.00%		4,412,6484,412,6485480Bracken species-level abundance
SRR28395739Candida parapsilosis
100.00%		6,047,5566,047,5565480Bracken species-level abundance
SRR28395740Candida parapsilosis
99.97%		5,301,5295,301,5295480Bracken species-level abundance

6. MEGAHIT assembly summary

SamplecontigsTotal bpN50Largest contig
SRR2839572739612,929,450112,532421,720
SRR2839572840412,941,711105,599315,881
SRR2839573240312,931,493103,078339,214
SRR2839573844912,947,09085,376237,575
SRR2839573940812,938,259110,836413,601
SRR2839574040612,936,473109,456315,906

7. Assembly quality assessment with QUAST

QUAST values are parsed from the native per-sample report.tsv format and transposed into one row per sample. This default surveillance mode reports QUAST assembly contiguity metrics such as contig count, total length, N50, largest contig, and GC percentage. It is very fast. BUSCO and Compleasm tasks are available as optional modules, but they are disabled by default in the recommended JSON and are not required for this QUAST-based assembly assessment.

Sample# contigsLargest contigTotal lengthGC (%)N50
SRR28395727396421,72012,929,45038.65112,532
SRR28395728404315,88112,941,71138.66105,599
SRR28395732403339,21412,931,49338.64103,078
SRR28395738449237,57512,947,09038.6485,376
SRR28395739408413,60112,938,25938.65110,836
SRR28395740406315,90612,936,47338.65109,456

8. Fungal antifungal-resistance characterization

This section reports mutation/gene-level evidence emitted by the configured fungal AMR container. A “No marker detected” result is not a susceptible call. Fluconazole resistance can be caused by ERG11 alterations, TAC1/UPC2/MRR1/PDR1-mediated efflux, aneuploidy/LOH, copy-number changes, species-specific mechanisms, or markers absent from the current AMR database.

Samplespeciesdrug_classdrugGene / statusmutationeffectevidence_levelinterpretation
SRR28395727Candida parapsilosisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR28395727.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR28395727.contigs
SRR28395728Candida parapsilosisazolefluconazole/other azolesCyp51R398IFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 R398I (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(NA/-1),Isavuconazole(NA/-1),Posaconazole(NA/-1),Voriconazole(NA/-1). Source: amr_out/SRR28395728.ChroQueTas/SRR28395728.contigs.ChroQueTaS.Cyp51.1.tsv:398
SRR28395732Candida parapsilosisazolefluconazole/other azolesCyp51Y132FFungAMR MUTATIONFungAMR curated marker detected by ChroQueTasCurated ChroQueTas/FungAMR marker detected: Cyp51 Y132F (FungAMR MUTATION). Drug evidence from ChroQueTas: Fluconazole(1/NA),Isavuconazole(NA/-1),Posaconazole(NA/-1),Voriconazole(1/-8). Source: amr_out/SRR28395732.ChroQueTas/SRR28395732.contigs.ChroQueTaS.Cyp51.1.tsv:132
SRR28395738Candida parapsilosisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR28395738.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR28395738.contigs
SRR28395739Candida parapsilosisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR28395739.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR28395739.contigs
SRR28395740Candida parapsilosisazole/otherfluconazole/otherNo marker — not susceptibleNANAscanner_detected_candidate_markerThe AMR scanner produced text consistent with a possible curated resistance marker, but rc151 could not parse an exact ChroQueTas marker row. Review fungal_amr.raw.tsv and fungal_amr.log for the exact record: amr_out/SRR28395740.ChroQueTas.AMR_summary.tsv No AMR mutations found in SRR28395740.contigs

9. Species-aware core-SNP phylogeny

When enabled, rMAP-Candida builds phylogenies separately for each species with sufficient samples and a matching reference. Mixed-species phylogenies are intentionally avoided. Outputs include species-group summaries, core-SNP alignments, and IQ-TREE Newick trees.

SpeciesStatusSamplesVariant-calling branchPloidy modelCore variable sitesNotes
Candida parapsilosisSKIPPED_SPECIES_NOT_IN_REFERENCE_MANIFEST6NANANASkipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.
Species without a displayed tree:
  • Candida parapsilosis: SKIPPED_SPECIES_NOT_IN_REFERENCE_MANIFEST; samples after species-specific consensus/eligibility = 6; branch = NA; note = Skipped by rc172 phylogeny guard because this detected species is not among the defined Candida species with an exported reference FASTA. Valid species with references are still processed.
Phylogeny interpretation note: rMAP-Candida builds one tree per species. Mixed-species Candida phylogenies are intentionally avoided. Treat these trees as species-level genomic relatedness visualizations unless recombination filtering and epidemiologic metadata support transmission interpretation.

10. Species-aware pairwise SNP distances and closest-neighbor summary

No core-SNP alignment was available for pairwise SNP-distance calculation.

11. Output navigation and provenance

The workflow emits downloadable tabular outputs in addition to this integrated HTML report.

rMAP-Myc-Candida-Candida_summary.tsv
rMAP_Candida_surveillance_summary.tsv
rMAP_Candida_pairwise_snp_distances.tsv
rMAP-Myc-Candida | Rapid Mycological Analysis Pipeline for Candida