ArticleNucleic acids research2020
Rapid, robust plasmid verification by de novo assembly of short sequencing reads.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Retrospective analysis and decentralized distribution to improve the lifecycle of Ah receptor research assets.Biochemical pharmacology · 2025Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.ACS synthetic biology · 2024Article
- Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.Nucleic acids research · 2024Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.bioRxiv : the preprint server for biology · 2024Article
- PlasCAT: Plasmid Cloud Assembly Tool.Bioinformatics (Oxford, England) · 2024Article
- Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences.PloS one · 2024Article
- ArrayedbioRxiv : the preprint server for biology · 2023Article
- Multiplexed long-read plasmid validation and analysis using OnRamp.Genome research · 2023Article
- Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device.BMC bioinformatics · 2023Article
- Multiplexed Assembly and Annotation of Synthetic Biology Constructs Using Long-Read Nanopore Sequencing.ACS synthetic biology · 2022Article
- Imaging translational control by Argonaute with single-molecule resolution in live cells.Nature communications · 2022Article
- Antimicrobial susceptibilities and comparative whole genome analysis of two isolates of the probiotic bacterium Lactiplantibacillus plantarum, strain ATCC 202195.Scientific reports · 2021Article
- Home-made enzymatic premix and Illumina sequencing allow for one-step Gibson assembly and verification of virus infectious clones.Phytopathology research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.