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

PeerJ

article

Anna Czmil¹  Michal Wronski¹  Sylwester Czmil¹  Marta Sochacka-Pietal²  Michal Cmil¹  Jan Gawor³  Tomasz Wołkowicz⁴  Dariusz Plewczynski⁵  Dominik Strzalka¹  Michal Pietal¹ 

[1] Department of Complex Systems, Rzeszow University of Technology;Department of Biotechnology and Bioinformatics, Rzeszow University of Technology;DNA Sequencing and Oligonucleotide Synthesis Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences;Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene;Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw;Laboratory of Bioinformatics and Computational Genomics, Warsaw University of Technology

关键词: NGS;    Bioinformatics;    Oxford Nanopore;    Genomics;    Webserver;    DNA sequencing;    DNA assembly;    Microbial genomes;   

DOI  :  10.7717/peerj.13056

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundNext 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.ResultsWe 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).

【 授权许可】

CC BY