Candida auris gene annotations

A Hybrid assembly of Illumina and nanopore reads was performed for C. auris using SPAdes version 3.9.0, with default k-mer lengths and 1D scaffolding. Annotation was achieved using Genemark, BLASTx against Swissprot and KEGG, and HMMER hmmscan against PFAM and TIGRFAM. We also ran tRNAscan and Rnammer to identify non-protein coding genes. Gene predictions were checked for a variety of issues including overlapping non-coding genes, overlaps coding genes, and containing in-frame stops. Genes were names according to BLAST and hmmer evidence in the following order of precedence: (1) Swissprot, (2) TIGRfam, and (3) KEGG, where BLAST hits must meet the 70% identity and 70% overlap criteria to be considered a good hit and for the name to be applied. Otherwise, genes are named hypothetical protein.