Record Details

MinION nanopore sequencing accelerates progress towards ubiquitous genetics in water research

CGSpace

View Archive Info
 
 
Field Value
 
Title MinION nanopore sequencing accelerates progress towards ubiquitous genetics in water research
 
Creator Werner, D.
Acharya, K.
Blackburn, A.
Zan, R.
Plaimart, J.
Allen, B.
Mgana, S. M.
Sabai, S. M.
Halla, F. F.
Massawa, S. M.
Haile, Alemseged Tamiru
Hiruy, A. M.
Mohammed, J.
Vinitnantharat, S.
Thongsamer, T.
Pantha, K.
Filho, C. R. M.
Lopes, B. C.
 
Subject water
research
biomass
bioinformatics
sustainable development goals
goal 6 clean water and sanitation
 
Description In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications.
 
Date 2022-08-12
2022-12-31T20:18:22Z
2022-12-31T20:18:22Z
 
Type Journal Article
 
Identifier Werner, D.; Acharya, K.; Blackburn, A.; Zan, R.; Plaimart, J.; Allen, B.; Mgana, S. M.; Sabai, S. M.; Halla, F. F.; Massawa, S. M.; Haile, Alemseged Tamiru; Hiruy, A. M.; Mohammed, J.; Vinitnantharat, S.; Thongsamer, T.; Pantha, K.; Filho, C. R. M.; Lopes, B. C. 2022. MinION nanopore sequencing accelerates progress towards ubiquitous genetics in water research. Water, 14(16):2491. (Special issue: Field Methods for Water Quality Surveying) [doi: https://doi.org/10.3390/w14162491]
2073-4441
https://hdl.handle.net/10568/126405
https://www.mdpi.com/2073-4441/14/16/2491/pdf?version=1660812648
https://doi.org/10.3390/w14162491
H051555
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format 14(16):2491. (Special issue: Field Methods for Water Quality Surveying)
 
Source Water