NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology

Abstract

Background Next Generation Sequencing (NGS) techniques dominate today’s landscape of genetics and genomics research. Though Illumina still dominates worldwide sequencing, Oxford Nanopore is one of the leading technologies currently being used by biologists, medics and geneticists across various applications. Oxford Nanopore is automated and relatively simple for conducting experiments, but generates gigabytes of raw data, to be processed by often ambiguous set of alternative bioinformatics command-line tools, and genomics frameworks which require a knowledge of bioinformatics to run. Results We established an inter-collegiate collaboration across experimentalists and bioinformaticians in order to provide a novel bioinformatics tool, free for academics. This tool allows people without extensive bioinformatics knowledge to simply process their raw genome sequencing data. Currently, due to ICT resources’ maintenance reasons, our server is only capable of handling small genomes (up to 15 Mb). In this paper, we introduce our tool, NanoForms: an intuitive and integrated web server for the processing and analysis of raw prokaryotic genome data, coming from Oxford Nanopore. NanoForms is freely available for academics at the following locations: http://nanoforms.tech (webserver) and https://github.com/czmilanna/nanoforms (GitHub source repository).

Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 genome for determining anti-Candida auris and anti-Candida albicans potential by pathogenicity and comparative genomics analysis

“…At the Institute for Research and Medical Consultations (IRMC), the whole bacterial genome of strain MR14M3 was sequenced with Oxford Nanopore long-read sequencing and initially analyzed using Nanopore Minion Epi2ME software (Oxford Nanopore Technologies-ONT, Oxford, UK) to calculate the coverage and quality of long reads generated using Oxford Nanopore long-read sequencing and converted to fastQ files for further analysis. Furthermore, Nanoforms and NanoGalaxy were used to assemble and annotate the obtained long-read sequence of MR14M3 [42] , [43] . To perform genome-based taxonomic classification using the generated whole-genome data, MR14M3 genome sequences were uploaded to TYGS (Type Strain Genome Server) ( https://tygs.dsmz.de/ ) and the Pathosystem Resource Integration Center (PATRIC) (BV-BRC 3.28.5), and a phylogenetic tree of MR14M3 was constructed using the whole genome [44] , [45] .…”

Prevalence of Plasmid-Mediated Quinolone Resistance (PMQRs) Determinants and Whole Genome Sequence Screening of PMQR-Producing E. coli Isolated from Men Undergoing a Transrectal Prostate Biopsy

“…Libraries for another 15 strains were prepared using a Nanopore Rapid Barcoding Kit, and the whole genome sequencing was performed on GridION (Oxford Nanopore Technologies, Oxford, UK). Genomes were assembled using CLC Genomics Workbench 22 (for strains sequenced on Illumina) and the NanoForms server (for strains sequenced on Nanopore [ 34 ]). Species confirmation, multilocus sequence typing (MLST), serotyping, virulence and AMR (Antimicrobial Resistance) genes, and plasmid replicons were analysed using SpeciesFinder 2.0 [ 35 ], MLST 2.0 [ 36 ], SerotyperFinder 2.0 [ 37 ], VirulenceFinder 2.0 [ 38 ], ResFinder 4.1 [ 39 ], respectively, available on the Centre for Genomic Epidemiology website ( , accessed on 1 January 2022).…”

Whole Genome Sequencing: Applications in Clinical Bacteriology

“…Routine clinical bacteriology applications can be performed through in-built platforms within the sequencers. These in-built platforms integrate pipelines, leading to automated data processing by the installed software that displays the results graphically [ 111 ].…”