CLONEQC: Lightweight sequence verification for synthetic biology

Pablo A. Lee, Jessica S. Dymond, Lisa Z. Scheifele, Sarah M. Richardson, Katrina J. Foelber, Jef D. Boeke, Joel S. Bader

Research output: Contribution to journalArticle

Abstract

Synthetic biology projects aim to produce physical DNA that matches a designed target sequence. Chemically synthesized oligomers are generally used as the starting point for building larger and larger sequences. Due to the error rate of chemical synthesis, these oligomers can have many differences from the target sequence. As oligomers are joined together to make larger and larger synthetic intermediates, it becomes essential to perform quality control to eliminate intermediates with errors and retain only those DNA molecules that are error free with respect to the target. This step is often performed by transforming bacteria with synthetic DNA and sequencing colonies until a clone with a perfect sequence is identified. Here we present CLONEQC, a lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server generates summary statistics (error rates and success rates target-bytarget) and a detailed report of perfect clones. This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere.net/ and as Berkeley Software Distribution (BSD) licensed source.

Original languageEnglish (US)
Article numbergkq093
Pages (from-to)2617-2623
Number of pages7
JournalNucleic Acids Research
Volume38
Issue number8
DOIs
StatePublished - Mar 6 2010

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Synthetic Biology
Clone Cells
Software
Quality Control
DNA
DNA Sequence Analysis
Bacteria

ASJC Scopus subject areas

  • Genetics

Cite this

Lee, P. A., Dymond, J. S., Scheifele, L. Z., Richardson, S. M., Foelber, K. J., Boeke, J. D., & Bader, J. S. (2010). CLONEQC: Lightweight sequence verification for synthetic biology. Nucleic Acids Research, 38(8), 2617-2623. [gkq093]. https://doi.org/10.1093/nar/gkq093

CLONEQC : Lightweight sequence verification for synthetic biology. / Lee, Pablo A.; Dymond, Jessica S.; Scheifele, Lisa Z.; Richardson, Sarah M.; Foelber, Katrina J.; Boeke, Jef D.; Bader, Joel S.

In: Nucleic Acids Research, Vol. 38, No. 8, gkq093, 06.03.2010, p. 2617-2623.

Research output: Contribution to journalArticle

Lee, PA, Dymond, JS, Scheifele, LZ, Richardson, SM, Foelber, KJ, Boeke, JD & Bader, JS 2010, 'CLONEQC: Lightweight sequence verification for synthetic biology', Nucleic Acids Research, vol. 38, no. 8, gkq093, pp. 2617-2623. https://doi.org/10.1093/nar/gkq093
Lee PA, Dymond JS, Scheifele LZ, Richardson SM, Foelber KJ, Boeke JD et al. CLONEQC: Lightweight sequence verification for synthetic biology. Nucleic Acids Research. 2010 Mar 6;38(8):2617-2623. gkq093. https://doi.org/10.1093/nar/gkq093
Lee, Pablo A. ; Dymond, Jessica S. ; Scheifele, Lisa Z. ; Richardson, Sarah M. ; Foelber, Katrina J. ; Boeke, Jef D. ; Bader, Joel S. / CLONEQC : Lightweight sequence verification for synthetic biology. In: Nucleic Acids Research. 2010 ; Vol. 38, No. 8. pp. 2617-2623.
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