Before proceeding with genome assembly, it is necessary to determine the appropriate strategy. In the scientific literature on whole genome sequencing applied to dermatophytes, some authors indicate that they proceeded with SPAdes followed by correction with Pilon, others indicate that they corrected the assembly with Bayes Hammer, the correction module included in SPAdes. Still others used MEGAHIT for their de novo assembly. To determine the best approach, 6 assembly strategies were used to assemble the genome of a single strain: KE005. The resulting assemblies are then compared to each other in order to determine, based on several metrics, which approach gives the best assembly. This evaluation is performed with QUAST.
The 6 strategies are as follows :
01_SP_unc : assembled with SPAdes but not corrected
02_SP_cor_BH : assembled with SPAdes and corrected with Bayes Hammer
03_SP_cor_PI : assembled with SPAdes and corrected with Pilon
04_MG_unc : assembled with MEGAHIT but not corrected
05_MG_cor_PI : assembled with MEGAHIT and corrected with Pilon
06_WT : assembled with WGS Typer
This workflow considers that the user directory (~/) is structured as seen in the "setting up the working environment" protocol. To avoid error messages, please follow this protocol and set up your computer before starting.