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
Affiliations
Anna Czmil
Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland
Michal Wronski
Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland
Sylwester Czmil
Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland
Marta Sochacka-Pietal
Department of Biotechnology and Bioinformatics, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland
Michal Cmil
Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland
Jan Gawor
DNA Sequencing and Oligonucleotide Synthesis Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Masovian, Poland
Tomasz Wołkowicz
Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, Warsaw, Masovian, Poland
Dariusz Plewczynski
Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Masovian, Poland
Dominik Strzalka
Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland
Michal Pietal
Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, Poland
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).
