Nanopore Sequencing and Genome Assembly

DNA was isolated using a DNeasy UltraClean microbial kit (Qiagen, Venlo, The Netherlands). Nanopore sequencing was performed according to protocol SQK-RBK110.96 with Flow Cell version R9.4.1 on a MinION device (FLO-MIN106D; Oxford Nanopore, Oxford, UK), using the super-accurate base-calling method in MinKNOW v22.12.7. Reads were trimmed and downsampled to 200× coverage using filtlong (https://github.com/rrwick/Filtlong, accessed on 6 January 2024) and assembled into circular contigs using Flye v2.9.1 [52 (link)]. Genomes were polished using Medaka v.1.1.0 (https://github.com/nanoporetech/medaka, accessed on 6 January 2024) and Homopolish (https://github.com/ythuang0522/homopolish?tab=readme-ov-file, accessed on 6 January 2024) [53 (link)] and annotated using Prokka v1.14.5 [54 (link)].

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Dec M., Zomer A., Webster J., Nowak T., Stępień-Pyśniak D, & Urban-Chmiel R. (2024). Integrative and Conjugative Elements and Prophage DNA as Carriers of Resistance Genes in Erysipelothrix rhusiopathiae Strains from Domestic Geese in Poland. International Journal of Molecular Sciences, 25(9), 4638.

Publication 2024

DNeasy UltraClean microbial kit FLO-MIN106D

Corresponding Organization : University of Life Sciences in Lublin

Other organizations : Utrecht University, New South Wales Department of Primary Industries

Top 5 similar protocols

Variable analysis

independent variables

DNA isolation method (DNeasy UltraClean microbial kit)

dependent variables

Sequence reads
Assembled circular contigs
Polished genomes
Annotated genomes

control variables

Nanopore sequencing protocol (SQK-RBK110.96)
Flow Cell version (R9.4.1)
Sequencing device (MinION)
Base-calling method (super-accurate in MinKNOW v22.12.7)
Read trimming and downsampling (Filtlong)
Genome assembly (Flye v2.9.1)
Genome polishing (Medaka v.1.1.0, Homopolish)
Genome annotation (Prokka v1.14.5)

Annotations

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