WGS of Candida parapsilosis: antifungal resistant
Genomic DNA for library preparation was isolated using Qiagen Genomic-tip 100/G kit (Qiagen) following the manufacturerŐs Genomic DNA Preparation instructions. Paired end DNA sequence libraries for Isolate 1 and Isolate 2 were prepared and sequenced using the Ion Proton Torrent sequencer and aligned to the C. parapsilosis CDC317 reference genome. The GATK Best Practices work flow was used, incorporating the following tools: bwa (193) v0.5.9 (aln and sample), Picard tools (http://picard.sourceforge.net) v1.107 (SortSam and MarkDuplicates), samtools (194) v0.1.19 and GATK (195) v2.8.  (RealignerTargetCreateor, IndelRealigner, BaseRecalibrator, PrintReads, ReduceReads, HaplotypeCaller).