Clinical and molecular epidemiology of carbapenemase-producing Enterobacterales in hospitalized patients

# Wiki

# Data location: 

The data was transferred from Athena medmicro):

``` 

/MedMicro/Clinton/CRE Pfizer Feb 2022/CRE study_1A_results_17022022 

/MedMicro/Clinton/CRE Pfizer Feb 2022/CRE study_1B_results_21022022

```

to Ilifu:

```

/scratch3/users/katiel/Clinton/CRE_study_August_2022/

```

#Reference data:

Klebsiella pneumoniae – strain HS11286 (GenBank accession no. CP003200.1) (n=18); 

Serratia marcescens – strain KS10 (GenBank accession no. CP027798.1) (n=3); 

Escherichia coli – strain ATCC 25922 (GenBank accession no. CP009072.1) (n=1); and 

Enterobacter cloacae – strain ATCC 13047 (GenBank accession no. NC_014121.1) (n=1).

```

/scratch3/users/katiel/Clinton/CRE_study_August_2022/ref_genomes

```

#Objectives workflow:

![workflow.png]()

#QC:

11 sample failed QC phred scores before trimming and filtering; none failed after filtering and trimming. Filtering and trimming were executed as follows:

```

nextflow run kviljoen/fastq_QC --reads '/scratch3/users/katiel/Clinton/CRE_study_August_2022/raw/study_1A_B_combined/*_R{1,2}_001.fastq.gz' -profile ilifu

```

QC reports can be found in the 'files' tab