NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology
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 appl...
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| Language: | English |
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PeerJ Inc.
2022-03-01
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| Online Access: | https://peerj.com/articles/13056.pdf |
| _version_ | 1827610964639350784 |
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| author | Anna Czmil Michal Wronski Sylwester Czmil Marta Sochacka-Pietal Michal Cmil Jan Gawor Tomasz Wołkowicz Dariusz Plewczynski Dominik Strzalka Michal Pietal |
| author_facet | Anna Czmil Michal Wronski Sylwester Czmil Marta Sochacka-Pietal Michal Cmil Jan Gawor Tomasz Wołkowicz Dariusz Plewczynski Dominik Strzalka Michal Pietal |
| author_sort | Anna Czmil |
| collection | DOAJ |
| description | 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). |
| first_indexed | 2024-03-09T07:58:17Z |
| format | Article |
| id | doaj.art-2bed06504d03432dbda4dd5645627c8d |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:58:17Z |
| publishDate | 2022-03-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-2bed06504d03432dbda4dd5645627c8d2023-12-03T00:49:47ZengPeerJ Inc.PeerJ2167-83592022-03-0110e1305610.7717/peerj.13056NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technologyAnna Czmil0Michal Wronski1Sylwester Czmil2Marta Sochacka-Pietal3Michal Cmil4Jan Gawor5Tomasz Wołkowicz6Dariusz Plewczynski7Dominik Strzalka8Michal Pietal9Department of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, PolandDepartment of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, PolandDepartment of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, PolandDepartment of Biotechnology and Bioinformatics, Rzeszow University of Technology, Rzeszow, Subcarpathian, PolandDepartment of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, PolandDNA Sequencing and Oligonucleotide Synthesis Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Masovian, PolandDepartment of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, Warsaw, Masovian, PolandLaboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Masovian, PolandDepartment of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, PolandDepartment of Complex Systems, Rzeszow University of Technology, Rzeszow, Subcarpathian, PolandBackground 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).https://peerj.com/articles/13056.pdfNGSBioinformaticsOxford NanoporeGenomicsWebserverDNA sequencing |
| spellingShingle | Anna Czmil Michal Wronski Sylwester Czmil Marta Sochacka-Pietal Michal Cmil Jan Gawor Tomasz Wołkowicz Dariusz Plewczynski Dominik Strzalka Michal Pietal NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology PeerJ NGS Bioinformatics Oxford Nanopore Genomics Webserver DNA sequencing |
| title | NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology |
| title_full | NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology |
| title_fullStr | NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology |
| title_full_unstemmed | NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology |
| title_short | NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology |
| title_sort | nanoforms an integrated server for processing analysis and assembly of raw sequencing data of microbial genomes from oxford nanopore technology |
| topic | NGS Bioinformatics Oxford Nanopore Genomics Webserver DNA sequencing |
| url | https://peerj.com/articles/13056.pdf |
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