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oligon-design

Simple and versatile tool to design specific oligonucleotides from large environmental datasets

https://github.com/miguelmsandin/oligon-design

Science Score: 67.0%

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    Found 3 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (11.7%) to scientific vocabulary
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Repository

Simple and versatile tool to design specific oligonucleotides from large environmental datasets

Basic Info
  • Host: GitHub
  • Owner: MiguelMSandin
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 8.06 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 3
  • Releases: 3
Created over 4 years ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

oligoN-design

DOI install with bioconda

The purpose of this tool is to help the user design specific oligonucleotide, to be later used as probes for Fluorescence in situ Hybridisation (FISH) or primers for PCR amplification. It focuses on Small SubUnit (SSU) of the rDNA operon (18S rDNA and 16S rDNA), but can potentially be used for other genes.

For a detailed documentation of the OligoN-design tool, please see the documentation.

brief_pipeline

Installation

OligoN-design is available from bioconda, and the simplest option to install oligoN-design is to use micromamba (or conda or mamba). So before starting, please make sure you have micromamba installed.
Once micromamba is installed, open the bash terminal, go to your preferred environment and run:
bash micromamba install oligon-design

Otherwise, you can create a new environment as follows: bash micromamba create --name oligoNenv oligon-design Then simply activate the environment to run oligoN-design functions (micromamba activate oligoNenv ), and deactivate it to exit (‘micromamba deactivate’).
Please, note that you can replace oligoNenv by the environment name of your choice.

For further information about installation, see the bioconda webapge.

Running

After activating the oligoN-design environment, you can start running the functions as follow: bash oligoNdesign -t target.fasta -e excluding.fasta -o oligos

Citing

We are preparing a manuscript that will soon be publicly available.

Concluding remarks

The OligoN-design tool was designed to help the design of specific oligonucleotides accommodating the large environmental datasets and with a simple and versatile approach. However, any output from this tool should be interpreted as a starting point and needs to be empirically optimized and tested.

Owner

  • Login: MiguelMSandin
  • Kind: user

PostDoc on the eco-evolution of Protist. Interested in molecular diversity and evolution. Not a (bio)informatician.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Sandin"
  given-names: "Miguel M"
  orcid: "https://orcid.org/0000-0002-0602-7613"
- family-names: "Walde"
  given-names: "Marie"
  orcid: "https://orcid.org/0000-0002-4071-7677"
title: "oligoN-design v0.3.0: A pipeline for the high throughput design of specific primers/probes"
doi: 10.5281/zenodo.7473220
version: v0.3.0
date-released: 2024-02-21
url: "https://github.com/MiguelMSandin/oligoN-design"

GitHub Events

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Last Year
  • Issues event: 3
  • Push event: 13
  • Pull request event: 5
  • Fork event: 1
  • Create event: 2