Introduction

Open Repository of Scripts and Resources for CycloneSEQ (CS1 and CS2) and Oxford Nanopore Technologies (R9.4.1 and R10.4.1) benchmarking.

Quick links

Scripts and pipeline

Genomics

The Giraffe documentation for read quality assessment.

The Flye usage for bacterial genome assembly and Racon usage for both long- and short-read polishing.

The BUSCO software for genome completeness assessment.

The QUAST software for mismatches among assemblies.

Epigenomics

The Hammerhead documentation for de novo bacterial methylation detection by stand-specific errors.

The adapted Bonito software for CycloneSEQ reads move table generation.

The NanoCurEA software for CycloneSEQ reads event generation.

The NanoCEM software for nanopore current signal comparison visualization.

Results

All the files can be found on figshare.

Observed read accuracy tables are available here.

Estimated read accuracy tables are available here.

Genome assemblies (WGS CS1 with NGS polishing）are available here.

Genome assemblies（WGS CS1 without NGS polishing）are available here.

Genome assemblies（WGS CS2 with NGS polishing）are available here.

Genome assemblies（WGS CS2 without NGS polishing）are available here.

Genome assemblies (WGA CS1 with NGS polishing）are available here.

Genome assemblies（WGA CS1 without NGS polishing）are available here.

Genome assemblies（WGA CS2 with NGS polishing）are available here.

Genome assemblies（WGA CS2 without NGS polishing）are available here.

The Quast results are available here.

The Busco results are available here.

The MEME results (20 bp units enrichment) are available here.

The MEME results (30 bp units enrichment) are available here.

Resource

• Basecall model for CycloneSEQ reads, using Bonito.
• All the FASTQ data is available here.
• The CycloneSEQ raw current signal of E. coli plasmid is available here.

Taxonomy

Kingdom	Phylum	Class	Order	Family	Genus	Species
Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter	Acinetobacter pittii
Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli
Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Klebsiella	Klebsiella pneumoniae
Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	Pseudomonas aeruginosa
Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Salmonella	Salmonella enterica
Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	Enterococcus faecium