Reference genomes
Reference genomes for C. auris clades were selected from Suphavilai et al., Discovery of the sixth Candida auris clade in Singapore (medRxiv) and include two (nearly) completed genomes per clade, if freely available from NCBI. For Clade V only one (nearly) complete genome was available from NCBI. Related species were selected from figure 3 of Muñoz et al., Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species (NatComm). Representative genomes were downloaded from NCBI. The sketch was constructed using sketch size 50,000 and k-mer size 27.
If you are missing new clades or have other reference genomes that would be good to include, please open an issue on GitHub.
The following reference genomes are included in the default database:
| filename | clade |
|---|---|
| refs/GCA_002759435.2_Candida_auris_CladeI.fna | Clade I |
| refs/GCA_002775015.1_Candida_auris_CladeIII.fna | Clade III |
| refs/GCA_003013715.2_Candida_auris_CladeII.fna | Clade II |
| refs/GCA_003014415.1_Candida_auris_CladeIV.fna | Clade IV |
| refs/GCA_008275145.1_Candida_auris_CladeIV.fna | Clade IV |
| refs/GCA_014217455.1_Candida_auris_CladeIII.fna | Clade III |
| refs/GCA_014673535.1_Candida_auris_CladeI.fna | Clade I |
| refs/GCA_016495665.1_Candida_auris_CladeII.fna | Clade II |
| refs/GCA_016809505.1_Candida_auris_CladeV.fna | Clade V |
| refs/GCA_032367535.1_Candida_auris_CladeVI.fna | Clade VI |
| refs/GCA_032715285.1_Candida_auris_CladeVI.fna | Clade VI |
| refs/GCF_000002545.3_Nakaseomyces_glabratus.fna | outgroup |
| refs/GCF_000003835.1_Clavispora_lusitaniae.fna | outgroup |
| refs/GCF_000006335.3_Candida_tropicalis.fna | outgroup |
| refs/GCF_000006445.2_Debaryomyces_hansenii.fna | outgroup |
| refs/GCF_000026945.1_Candida_dubliniensis.fna | outgroup |
| refs/GCF_000149425.1_Meyerozyma_guilliermondii.fna | outgroup |
| refs/GCF_000149685.1_Lodderomyces_elongisporus.fna | outgroup |
| refs/GCF_000182765.1_Candida_parapsilosis.fna | outgroup |
| refs/GCF_000182965.3_Candida_albicans.fna | outgroup |
| refs/GCF_000315875.1_Candida_orthopsilosis.fna | outgroup |
| refs/GCF_002926055.2_Candida_haemulonii.fna | outgroup |
| refs/GCF_003013735.1_Candida_pseudohaemulonii.fna | outgroup |
| refs/GCF_003054445.1_Pichia_kudriavzevii.fna | outgroup |