Methylation-free E.coli nanopore sequencing (ONT R9.4.1) data set
DOI10.5281/zenodo.7995806Zenodo7995806MaRDI QIDQ6695760FDOQ6695760
Dataset published at Zenodo repository.
Xuechun Xu, Patrik Ståhl, Joakim Jaldén, Nayanika Bhalla
Publication date: 29 May 2023
Copyright license: Creative Commons Attribution 4.0 International
The data set consists offast5 files divided into5 zip files(fast5_[1-5].zip), a genome record (Ecoli_K12_MG1655.fasta), an Illumina assembly genome (illumina_contigs.fasta)and a fastq filefrom Guppy 5 (guppy_basecalled.fastq.gz).We sequencedthe Ecoli non-methylated genomic DNA (D5016, Zymo Research) with an ONT MinION device. The sequencing libraries were preparedby fragmenting the genomic DNA using Covaris g-TUBE and a Ligation sequencing kit (SQK-LSK109, Oxford Nanopore) with Flow Cell chemistry R9.4.1. We also performed short-read Illumina sequencing on the same sample using the TruSeq PCR-free library preparation on the MiSeq sequencing platform (Illumina, USA), andconstructed a draft assembly from the Illumina sequencing results using SPAdes v3.6.0. We also upload a reference genome directly obtained from the E.coli sample producer website. In addition, the data set contains two fastq files that produced bytheLokatt basecaller (lokatt_basecalled.fasta.gz) and local-trained Bonito basecaller (bonito_local_basecalled.fastq.gz), respectively, which are used for benchmarking in the Lokatt basecaller paper.
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