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SpeciesPrimer: A bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species

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61 days ago
SpeciesPrimer: A bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species https://t.co/6r4JwFyPEh https://t.co/Jwg4RchM6t
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Supplemental Information

Pipeline input (Input genome assembly accessions, Pipeline configuration, Specieslist)

DOI: 10.7287/peerj.preprints.27870v1/supp-1

Bacterial strains (Target strains, Non-target strains, Cultivation conditions)

DOI: 10.7287/peerj.preprints.27870v1/supp-2

Summary of predicted-amplicon BLAST results

DOI: 10.7287/peerj.preprints.27870v1/supp-3

qPCR raw data

Raw data of qPCR experiments. Data export from Rotor-Gene 6000 Software 1.7 with dynamic tube normalization and a threshold of 0.05 for quantification cycle (Cq) value calculation, the five first cycles were ignored for the determination of the Cq values. The peak calling threshold for the melt curve analysis was set to -2 dF/dT and a temperature threshold was set 2 °C lower than the positive control peak.

DOI: 10.7287/peerj.preprints.27870v1/supp-4

Primer sequences of the qPCR assays used for the in vitro validation

DOI: 10.7287/peerj.preprints.27870v1/supp-5

Summary of primer-BLAST results

DOI: 10.7287/peerj.preprints.27870v1/supp-6

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Matthias Dreier conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Hélène Berthoud conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Noam Shani conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Daniel Wechsler conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Pilar Junier conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

Code is available at

https://github.com/biologger/speciesprimer

Docker image is available at

https://hub.docker.com/r/biologger/speciesprimer.

Funding

The authors received no funding for this work.


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