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