Securing the exchange of synthetic genetic constructs using digital signatures

Gallegos, Jenna E.; Kar, Diptendu Mohan; Ray, Indrakshi; Ray, Indrajit; Peccoud, Jean

doi:10.1101/750927

Cited by 3 publications

(2 citation statements)

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“…We built and tested our pipeline using Illumina sequencing reads from 96 plasmid DNA samples as previously described ( 19 ). Briefly, 6–24 individual transformants of eight different plasmids (ranging in size from 2521 to 3294 bp) were sequenced.…”

Section: Methodsmentioning

confidence: 99%

Rapid, robust plasmid verification by de novo assembly of short sequencing reads

Gallegos

Rogers²,

Cialek

et al. 2020

Nucleic Acids Research

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Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and—depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

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Section: Methodsmentioning

confidence: 99%

Rapid, robust plasmid verification by de novo assembly of short sequencing reads

Gallegos

Rogers²,

Cialek

et al. 2020

Nucleic Acids Research

Self Cite

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show abstract

“…The sequencing dataset used to develop our workflow was generated in conjunction with a separate publication. Detailed explanations and plasmid reference sequences can be found in that manuscript (19).…”

Section: Plasmid Preparation and Sequencingmentioning

confidence: 99%

Rapid, robust plasmid verification byde novoassembly of short sequencing reads

Gallegos

Rogers²,

Cialek

et al. 2020

Preprint

Self Cite

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AbstractPlasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and— depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

show abstract