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:

#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