Biofoundry-Scale DNA Assembly Validation Using Cost-Effective High-Throughput Long-Read Sequencing

Peter Vegh*, Sophie Donovan, Susan Rosser, Giovanni Stracquadanio, Rennos Fragkoudis*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Biofoundries are automated high-throughput facilities specializing in the design, construction, and testing of engineered/synthetic DNA constructs (plasmids), often from genetic parts. A critical step of this process is assessing the fidelity of the assembled DNA construct to the desired design. Current methods utilized for this purpose are restriction digest or PCR followed by fragment analysis and sequencing. The Edinburgh Genome Foundry (EGF) has recently established a single-molecule sequencing quality control step using the Oxford Nanopore sequencing technology, along with a companion Nextflow pipeline and a Python package, to perform in-depth analysis and generate a detailed report. Our software enables researchers working with plasmids, including biofoundry scientists, to rapidly analyze and interpret sequencing data. In conclusion, we have created a laboratory and software protocol that validates assembled, cloned, or edited plasmids, using Nanopore long-reads, which can serve as a useful resource for the genetics, synthetic biology, and sequencing communities.
Original languageEnglish
Pages (from-to)683-686
Number of pages4
JournalACS Synthetic Biology
Issue number2
Early online date8 Feb 2024
Publication statusPublished - 16 Feb 2024

Keywords / Materials (for Non-textual outputs)

  • biofoundry
  • DNA assembly
  • plasmid validation
  • sequencing


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