Input & output

Input

AuriClass takes an arbitrary number of Fastq or Fasta files as input (however not Fastq and Fasta in a single analysis). AuriClass assumes all files originate from a single sample.

Reference data (included)

Two files with reference data are needed to start the analysis. Default files are included:

File	Description
data/clade_config.csv	CSV table listing two columns: filename and associated clade. All included species that are not Candida auris are listed as "outgroup".
data/Candida_auris_clade_references.msh	Mash sketch of reference genomes of Candida auris and related species.

See Reference genomes for more information on the default database and see the FAQ for how to build your own database or change calibrated settings.

Output

AuriClass outputs a tab-separated text file containing the main output, and a log file which save info written to STDERR.

The columns in the output report have the following information:

Column	Description
Sample	Sample name. Default value is "isolate".
Clade	Predicted clade. If the closest sample is not Candida auris, this field will contain "not Candida auris".
Mash_distance_from_closest_reference	Mash distance from the closest reference genome.
QC_decision	"FAIL" is QC_species is "FAIL". "WARN" if any other QC step indicates "WARN". Otherwise "PASS".
QC_species	"FAIL" if the mash distance from the closest reference is more than --non_candida_threshold. This indicates that the sample is not closely related to any Candida spp.
QC_other_Candida	"WARN" if the closest reference genome is not a Candida auris reference genome. This indicates that the sample is closer to another species than Candida auris.
QC_genome_size	"WARN" if the estimated genome size is outside the specified range. This is probably not accurate in case you run a diploid sample.
QC_multiple_hits	"WARN" if at least one sample is within the 99% Mash error bounds of the closest hit (from mash bounds -k [KMERSIZE] -p 0.99). This should not happen if the appropriate settings and database are used.
QC_possible_new_clade	"WARN" if the closest reference genome is Candida auris, but the Mash distance is higher than the --new_clade_threshold.