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Title: Rapid, robust plasmid verification by de novo assembly of short sequencing reads
Abstract 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.  more » « less
Award ID(s):
1934573
PAR ID:
10302166
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Nucleic Acids Research
Volume:
48
Issue:
18
ISSN:
0305-1048
Page Range / eLocation ID:
e106 to e106
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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