Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification
Alexandre Lamas, Alejandro Garrido-Maestu, Alberto Prieto, Alberto Cepeda, Carlos Manuel Franco · 2023
Read Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification by Alexandre Lamas, Alejandro Garrido-Maestu, Alberto Prieto, Alberto Cepeda, Carlos Manuel Franco (2023) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-10722185.txt.
Description
Alexandre Lamas and four co-authors set up genome sequencing on a shoestring for food safety labs, in a 2023 paper. Reading a germ's whole genome is the sharpest tool for tracing outbreaks, but big sequencers and computing skill blocked small labs. A pocket-sized long-read device changes the entry cost.
Their workflow pairs the handheld sequencer with a free, web-based analysis platform that needs no coding. Settings are tuned for modest computers and single-use flow cells. The target is Salmonella: the pipeline names its serotype, flags its virulence genes, and lists drug resistance genes in one rapid run. A lab with basic gear can now answer, during an outbreak, questions that once required a national center.
Catalog record
| CREATOR | Alexandre Lamas, Alejandro Garrido-Maestu, Alberto Prieto, Alberto Cepeda, Carlos Manuel Franco |
|---|---|
| YEAR | 2023 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 52 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |