NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology.
Bioinformatics
DNA assembly
DNA sequencing
Genomics
Microbial genomes
NGS
Oxford Nanopore
Webserver
Journal
PeerJ
ISSN: 2167-8359
Titre abrégé: PeerJ
Pays: United States
ID NLM: 101603425
Informations de publication
Date de publication:
2022
2022
Historique:
received:
23
08
2021
accepted:
13
02
2022
entrez:
4
4
2022
pubmed:
5
4
2022
medline:
5
4
2022
Statut:
epublish
Résumé
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. 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).
Sections du résumé
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).
Identifiants
pubmed: 35368340
doi: 10.7717/peerj.13056
pii: 13056
pmc: PMC8973472
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Pagination
e13056Informations de copyright
©2022 Czmil et al.
Déclaration de conflit d'intérêts
The authors declare there are no competing interests.
Références
BMC Genomics. 2019 Jan 9;20(1):23
pubmed: 30626323
Gigascience. 2015 Dec 04;4:60
pubmed: 26640692
Genome Res. 2019 Jul;29(7):1178-1187
pubmed: 31186302
Cell. 2019 Aug 8;178(4):779-794
pubmed: 31398336
Genome Res. 2020 Jan;30(1):138-152
pubmed: 31809257
Gigascience. 2020 Oct 17;9(10):
pubmed: 33068114
Microb Genom. 2017 Sep 14;3(10):e000132
pubmed: 29177090
Sci Rep. 2018 Aug 13;8(1):12034
pubmed: 30104688
Genomics Proteomics Bioinformatics. 2015 Oct;13(5):278-89
pubmed: 26542840
BMC Genomics. 2020 Sep 14;21(1):631
pubmed: 32928108
Bioinformatics. 2018 Jul 1;34(13):i142-i150
pubmed: 29949969
Bioinformatics. 2015 Oct 15;31(20):3350-2
pubmed: 26099265
Nucleic Acids Res. 2010 Apr;38(6):1767-71
pubmed: 20015970
Genome Biol. 2016 Nov 25;17(1):239
pubmed: 27887629
Bioinformatics. 2017 Aug 15;33(16):2580-2582
pubmed: 28379341
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Genomics. 2021 Nov;113(6):4022-4027
pubmed: 34648882
Nucleic Acids Res. 2020 Jul 2;48(W1):W366-W371
pubmed: 32442274
PLoS Comput Biol. 2017 Jun 8;13(6):e1005595
pubmed: 28594827
Nat Biotechnol. 2020 Jun;38(6):701-707
pubmed: 32042169
Methods. 2013 Sep 1;63(1):41-9
pubmed: 23816787
Gigascience. 2019 Feb 1;8(2):
pubmed: 30689855
BMC Genomics. 2020 Jan 6;21(1):14
pubmed: 31906858
Genome Biol. 2017 Sep 21;18(1):182
pubmed: 28934964
BMC Bioinformatics. 2011 Sep 30;12:385
pubmed: 21961884
Methods Enzymol. 1990;183:63-98
pubmed: 2156132
Bioinformatics. 2018 Aug 1;34(15):2666-2669
pubmed: 29547981
PeerJ. 2013 Sep 17;1:e167
pubmed: 24109552
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Infect Immun. 2011 Nov;79(11):4286-98
pubmed: 21896772
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):E8396-E8405
pubmed: 27956617
Small. 2020 Aug;16(32):e2002169
pubmed: 32578378
PLoS One. 2010 Oct 26;5(10):e15406
pubmed: 21048977