Cauris_CladeTyper¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
| Standalone | Mycotics | v3.0.0 | Yes | Sample-level |
Cauris_CladeTyper_PHB¶
The Cauris_CladeTyper_PHB Workflow is designed to assign the clade to Candidozyma auris (also known as Candida auris) WGS assemblies based on their genomic sequence similarity to the five clade-specific reference files. Clade typing is essential for understanding the epidemiology and evolutionary dynamics of this emerging multidrug-resistant fungal pathogen.
Inputs¶
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| cauris_cladetyper | assembly_fasta | File | The assembly file for your sample in FASTA format | Required | |
| cauris_cladetyper | samplename | String | The name of the sample being analyzed | Required | |
| cladetyper | cpu | Int | Number of CPUs to allocate to the task | 8 | Optional |
| cladetyper | disk_size | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
| cladetyper | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/biocontainers/hesslab-gambit:0.5.1--py37h8902056_0 | Optional |
| cladetyper | kmer_size | Int | The kmer size to use for generating the GAMBIT signatures file; see GAMBIT documentation for more details | 11 | Optional |
| cladetyper | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 16 | Optional |
| cladetyper | ref_clade1 | File | The reference assembly for clade 1 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435.2_Cand_auris_B8441_V2_genomic.fasta | Optional |
| cladetyper | ref_clade1_annotated | String | The path to the annotated reference for clade 1 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade1_GCA_002759435_Cauris_B8441_V2_genomic.gbff | Optional |
| cladetyper | ref_clade2 | File | The reference assembly for clade 2 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.fasta | Optional |
| cladetyper | ref_clade2_annotated | String | The path to the annotated reference for clade 2 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade2_GCA_003013715.2_ASM301371v2_genomic.gbff | Optional |
| cladetyper | ref_clade3 | File | The reference assembly for clade 3 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.fasta | Optional |
| cladetyper | ref_clade3_annotated | String | The path to the annotated reference for clade 3 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade3_GCF_002775015.1_Cand_auris_B11221_V1_genomic.gbff | Optional |
| cladetyper | ref_clade4 | File | The reference assembly for clade 4 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.fasta | Optional |
| cladetyper | ref_clade4_annotated | String | The path to the annotated reference for clade 4 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade4_GCA_003014415.1_Cand_auris_B11243_genomic.gbff | Optional |
| cladetyper | ref_clade5 | File | The reference assembly for clade 5 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.fasta | Optional |
| cladetyper | ref_clade5_annotated | String | The path to the annotated reference for clade 5 | gs://theiagen-public-resources-rp/reference_data/eukaryotic/candidozyma/Cauris_Clade5_GCA_016809505.1_ASM1680950v1_genomic.gbff | Optional |
| version_capture | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0 | Optional |
| version_capture | timezone | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | Optional |
Workflow Tasks¶
Cladetyping: clade determination
The Cauris_Cladetyper Workflow for Candidozyma auris employs GAMBIT for taxonomic identification, comparing whole genome sequencing data against reference databases to accurately classify Candidozyma auris isolates.
A custom GAMBIT database is created using five clade-specific Candidozyma auris reference genomes. Sequences undergo genomic signature comparison against this database, which then enables assignment to one of the five Candidozyma auris clades (Clade I to Clade V) based on sequence similarity and phylogenetic relationships. This integrated approach ensures precise clade assignments, crucial for understanding the genetic diversity and epidemiology of Candidozyma auris.
See more information on the reference information for the five clades below:
| Clade | Genome Accession | Assembly Name | Strain | BioSample Accession |
|---|---|---|---|---|
| Clade I | GCA_002759435.2 | Cand_auris_B8441_V2 | B8441 | SAMN05379624 |
| Clade II | GCA_003013715.2 | ASM301371v2 | B11220 | SAMN05379608 |
| Clade III | GCA_002775015.1 | Cand_auris_B11221_V1 | B11221 | SAMN05379609 |
| Clade IV | GCA_003014415.1 | Cand_auris_B11243 | B11243 | SAMN05379619 |
| Clade V | GCA_016809505.1 | ASM1680950v1 | IFRC2087 | SAMN11570381 |
Cauris_Cladetyper Technical Details
Outputs¶
| Variable | Type | Description |
|---|---|---|
| cauris_cladetyper_wf_analysis_date | String | Date of analysis |
| cauris_cladetyper_wf_version | String | Version of PHB used for the analysis |
| cladetyper_annotated_reference | String | The annotated reference file for the identified clade, "None" if no clade was identified |
| cladetyper_clade | String | The clade assigned to the input assembly |
| cladetyper_docker_image | String | The Docker container used for the task |
| cladetyper_gambit_version | String | The version of GAMBIT used for the analysis |
References¶
Lumpe J, Gumbleton L, Gorzalski A, Libuit K, Varghese V, Lloyd T, et al. (2023) GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. PLoS ONE 18(2): e0277575. https://doi.org/10.1371/journal.pone.0277575
Ambrosio, Frank, Michelle Scribner, Sage Wright, James Otieno, Emma Doughty, Andrew Gorzalski, Danielle Siao, et al. 2023. "TheiaEuk: A Species-Agnostic Bioinformatics Workflow for Fungal Genomic Characterization." Frontiers in Public Health 11. https://doi.org/10.3389/fpubh.2023.1198213.