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

Anna Czmil; Michal Wronski; Sylwester Czmil; Marta Sochacka-Pietal; Michal Cmil; Jan Gawor; Tomasz Wołkowicz; Dariusz Plewczynski; Dominik Strzalka; Michal Pietal

doi:10.7717/peerj.13056

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

PeerJ. 2022 Mar 29:10:e13056. doi: 10.7717/peerj.13056. eCollection 2022.

Authors

Affiliations

¹ Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland.
² Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland.
³ DNA Sequencing and Oligonucleotide Synthesis Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Masovian, Poland.
⁴ Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, Warsaw, Masovian, Poland.
⁵ Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Masovian, Poland.
⁶ Laboratory of Bioinformatics and Computational Genomics, Warsaw University of Technology, Warsaw, Masovian, Poland.

^# Contributed equally.

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).

Keywords: Bioinformatics; DNA assembly; DNA sequencing; Genomics; Microbial genomes; NGS; Oxford Nanopore; Webserver.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computers
Genome, Microbial
Genomics / methods
Humans
Nanopores*
Sequence Analysis, DNA / methods

Grants and funding

The work of Dominik Strzalka, Michal Pietal, Michal Cmil, Marta Sochacka-Pietal, Michal Wronski and Anna Czmil as well as the paper itself, was financed by Subcarpatian Center for Innovation (Podkarpackie Centrum Innowacyjnos̀ci - PCI), Teofila Lenartowicza 4 Street, 35-051 Rzeszòw, Poland, under the grant no. F3_116 contract no. 05/PRZ/1/DG/PCI/2019. “Oxford Nanopore technology: optimization of enzymes and analysis of genomic data for commercial applications”. Michal Pietal and Dariusz Plewczynski were supported by the National Science Center grant (2018/02/X/NZ2/00622) “Identification of structural variants in the human genome using long fragments from next generation sequencing, based on Oxford Nanopore technology”. Dariusz Plewczynski was supported by Polish National Science Centre (2019/35/O/ST6/02484), and the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (TEAM to Dariusz Plewczynski) “Three-dimensional Human Genome structure at the population scale: computational algorithm and experimental validation for lymphoblastoid cell lines of selected families from 1000 Genomes Project”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.