Genomic Analysis of Keratitis-Associated S. Epidermidis and S. Warneri Isolates

1​‌‍‍‍‌‍‍‌‍‌‌‍‍‍‌‍‌‌‌‍​- Genome sequence keratitis-associated isolates, with particular reference to the species: S. epidermidis and S. warneri and develop skills for genomic analysis. 2. Determine the interactions between staphylococci from keratitis. Previous work has found an increased frequency of antimicrobial producers from particular niches and the study will incorporate ocular isolates to test for inhibition and novel antimicrobial activities based on experimental evolution and genome resequencing. The expression of haemolysin genes in some S. epidermidis strains has been established in research through genomic analysis. Gill et al. (2005) applied complete genome analysis to show that both methicillin-resistant S. aureus and S. epidermidis strains RP62a and ATCC 12228 express beta- and delta haemolysin genes. They reported that S. epidermidis RP62a expresses hlb and hld genes in the locus SE2544 and SE1489, respectively. The studies also show that S. epidermidis ATCC 12228 expresses hlb and hld genes in the locus SE0008 and SE1634 respectively (Gill, et al., 2005​‌‍‍‍‌‍‍‌‍‌‌‍‍‍‌‍‌‌‌‍​). In another genomic analysis, Zhang et al. (2003) compared virulence genes in S. epidermidis ATCC 12228 and S. aureus N315 showed that the two shares ?? haemolysin and haemolysin genes (Zhang, et al., 2003). The genomic analysis provides solid evidence that S. epidermidis may utilize haemolysins in its pathogenicity. 1- Present clear evidence of comparative genomics analysis of S. epidermidis isolates from keratitis, including sequencing Liverpool keratitis isolates – Assembly – Annotation – SNP – Phylogenetic tree what I need: 1-what the perpose of the genatic analysis and bioinformatic 2- what we locking for I’ll upload the files I need to explain what you can see on the file by Multi QC and linux (Programs I frequently use: Quality control and Pre-processing: FastQC-MultiQC ) • Assembly: o Unicycer o QUAST to analyse how good your assemblies are o Bandage to visualise how good assemblies are • Annotation: o Prokka • Phylogenetics: o Snipyy o IQTREE o Gubbins o Roary o Panaroo o Rhierbaps o Abricate o AM​‌‍‍‍‌‍‍‌‍‌‌‍‍‍‌‍‌‌‌‍​RFinder

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