Long read sequencing of carbapenemase producing bacteria

This data set consists of genome sequencing data of multi-resistant bacteria. These were sequenced using Illumina technology at the USB and using long-read nanopore technology at the Biozentrum. In addition, resistance data are available for these strains. The raw data have been deposited in public archives at NCBI under BioProject PRJEB28660.

illumina_data.tree

This file contains the directory listing of the trimmed short reads. The sample number is the first part of the file name. Files ending on _R1_001_val_1.fq.gz are read 1, files ending on _R2_001_val_2.fq.gz are read 2.

nanopore_data.tree

This file contains the nanopore runs (or rather the directory structure of these data). Each run is labeled by the date with the format %Y%m%d. Each folder contains the processed reads by barcode as BC{%02d}.fasta.gz where the placeholder is the barcode number.

sample_table.csv

This file contains the relevant linking information. The header line is

Internal #,Isolate #,Species,Labor Number,Date,Box,Platz,DNA Konzentration,sequenced,mb,barcode,resequenced,rebarcode

where Internal # is our consecutive index that is used to refer to the strains as carb001 etc. Labor Nummer is the number used to label the illumina data. sequenced and barcode are the fields that identify the nanopore data. Some samples have been resequenced on nanopore, these are labeled as resequenced and rebarcode are the fields that identify the nanopore data.

Note that the sample table only contains a subset of the strains. Fine to focus on these for now.

MIC_data.csv

This file contains more meta data such as species as well as resistance information.