Genomes plasmids MDR B. fragilis ONT sequence read files in fastq format

Supporting data for the manuscript Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids.

Oxford Nanopore reads demultiplexed with Deepbinner v0.2.0 and base-called (with demultiplexing) using Albacore v2.3.3. Barcodes and adapters were removed with Porechop v0.2.4 with the --discard_middle option.

Data from each isolate was produced from two runs per isolate. Data for the individual runs are included here. They can easily be concatenated eg with cat. Runs are named TVS_01,. TVS_02, TVS_03 and TVS_04.

Fast5 (only demultiplexed with deepbinner and basecalled with albacore) as well as illumina reads and genome assemblies can be found via the NCBI bioproject accessions:

Isolates, NCBI bioproject accession no:

CCUG4856T, PRJNA525024

BFO17, PRJNA244943

BFO18, PRJNA244944

S01, PRJNA244942

BFO42, PRJNA253771

BFO67, PRJNA254401

BFO85, PRJNA254455

md5sum's (also found in the file md5.md5):

135d0570a1e49e25c8fde59f321cca68  BFO17_TVS_03_99377.barcode02_trimmed.fastq.gz
3c6ca800a1f735937c0cffccd263fb82  BFO18_TVS_01_97673.barcode03_trimmed.fastq.gz
dc37823950f529d3a859b7a7c514af8c  BFO18_TVS_03_99377.barcode03_trimmed.fastq.gz
abd707404f9ebbc38652e45ed378ca21  BFO42_TVS_02.barcode10_trimmed.fastq.gz
9761e9ab082e276624c5778dcbeaffd2  BFO42_TVS_04.barcode10_trimmed.fastq.gz
ffc27009c0f7fead1af84ce045dbe5f3  BFO67_TVS_02.barcode09_trimmed.fastq.gz
06c363a7feeeb88f9d195b3769b37f2b  BFO67_TVS_04.barcode09_trimmed.fastq.gz
5553c95cc98f4b9d4cfb38c4f8f8f037  BFO85_TVS_02.barcode08_trimmed.fastq.gz
b1a8013cba7a079cee6d3bdd6cd97ff2  BFO85_TVS_04.barcode08_trimmed.fastq.gz
8169225219a5fb20935d5f0304aa80c5  CCUG4856T_TVS_01_97673.barcode01_trimmed.fastq.gz
a509b0ae912a798a91e677795198c1c6  CCUG5846T_TVS_03_99377.barcode01_trimmed.fastq.gz
8a9d2eb8b626a6e87ed267d31aa220e3  S01_TVS_01_97673.barcode04_trimmed.fastq.gz
69e239a17becc25a4f103dfc3bf5886a  S01_TVS_03_99377.barcode04_trimmed.fastq.gz