Repositories list

• DnaWeaver

  Public
  A route planner for DNA assembly

  synthetic-biologyplanningdna-assembly+ 1cloning-strategy

  Python

  •

  MIT License

  •9•31•8•1•Updated Mar 10, 2025Mar 10, 2025

• HowTo

  Public
  📒 Short opinionated recipes, mostly for us.

  Python

  •0•4•0•0•Updated Mar 3, 2025Mar 3, 2025

• genedom

  Public
  Batch domestication of genetic parts with Python

  synthetic-biologysynbiodna-assembly+ 2sequence-designpart-domestication

  Python

  •

  MIT License

  •1•16•0•0•Updated Feb 26, 2025Feb 26, 2025

• Sequeduct

  Public
  Sequencing analysis pipeline

  Nextflow

  •

  GNU General Public License v3.0

  •0•14•1•0•Updated Feb 18, 2025Feb 18, 2025

• DnaChisel

  Public
  ✏️ A versatile DNA sequence optimizer

  bioinformaticssynthetic-biologysynbio+ 3sequence-designdna-optimizationcodon-optimization

  Python

  •

  MIT License

  •46•229•13•1•Updated Feb 17, 2025Feb 17, 2025

• Ediacara

  Public
  Python package for interpreting sequencing data of assembled DNA constructs (plasmids)

  Python

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Feb 15, 2025Feb 15, 2025

• Dioscuri

  Public
  Python package for working with Gemini WorkList (gwl) files

  Python

  •

  MIT License

  •1•8•0•0•Updated Feb 7, 2025Feb 7, 2025

• Plasmid_assessor

  Public
  Plasmid assessment for Golden Gate cloning

  Python

  •

  MIT License

  •1•1•0•0•Updated Jan 28, 2025Jan 28, 2025

• codon-usage-tables

  Public
  📊 Codon usage tables in code-friendly format + Python bindings

  bioinformaticssynbiocodon-optimization+ 1codon-usage

  Python

  •

  Creative Commons Zero v1.0 Universal

  •10•35•0•0•Updated Jan 27, 2025Jan 27, 2025

• DnaFeaturesViewer

  Public
  👁️ Python library to plot DNA sequence features (e.g. from Genbank files)

  visualizationbioinformaticssynthetic-biology+ 3genbankmolecular-biologydna-visualization

  Python

  •

  MIT License

  •95•619•35•3•Updated Jan 9, 2025Jan 9, 2025

• easy_dna

  Public
  🎒 Python library to read, write, edit DNA sequences

  Python

  •

  MIT License

  •0•7•0•0•Updated Dec 18, 2024Dec 18, 2024

• Plateo

  Public
  🤖 Python biolab automation library: parsers, report generators, picklist simulators, and more

  parsersynthetic-biologylab-automation

  Python

  •

  MIT License

  •7•43•1•0•Updated Oct 4, 2024Oct 4, 2024

• Examples

  Public
  Collection of Python modules and Jupyter notebook examples

  HTML

  •

  MIT License

  •2•6•0•0•Updated Sep 5, 2024Sep 5, 2024

• Mutator

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Aug 13, 2024Aug 13, 2024

• Sequeduct_Methyl

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Aug 8, 2024Aug 8, 2024

• SnapGeneReader

  Public
  👓 Python library to parse Snapgene *.dna files to dict or biopython seqrecord.

  convertersynthetic-biologybiopython+ 3genbanksequence-designsnapgene

  Python

  •

  MIT License

  •15•19•0•0•Updated Aug 2, 2024Aug 2, 2024

• EpiJinn

  Public
  DNA methylation and restriction

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jul 11, 2024Jul 11, 2024

• Seq_Report

  Public
  Simple reporting on a set of sequences for documentation purposes

  Python

  •

  MIT License

  •0•1•0•0•Updated Apr 25, 2024Apr 25, 2024

• pdf_reports

  Public
  📕 Python library and CSS theme to generate PDF reports from HTML/Pug

  pythonpdfreporting

  Python

  •

  MIT License

  •40•229•12•0•Updated Apr 18, 2024Apr 18, 2024

• Sequeduct_demo

  Public
  Demonstration data for the Sequeduct pipeline

  HTML

  •1•5•0•0•Updated Feb 19, 2024Feb 19, 2024

• DnaCauldron

  Public
  ⚗️ Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies

  synthetic-biologymolecular-biologydna-assembly+ 2golden-gatecloning-simulator

  Python

  •

  MIT License

  •11•56•6•0•Updated Jul 28, 2023Jul 28, 2023

• Plater

  Public
  Package for generating picklist files

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 27, 2023Jul 27, 2023

• Caravagene

  Public
  🎨 Python library to plot multi-part genetic constructs

  synthetic-biologymolecular-biologydna-assembly+ 1sequence-design

  Python

  •

  MIT License

  •2•25•0•0•Updated Jul 21, 2023Jul 21, 2023

• crazydoc

  Public
  Read DNA sequences from colourful Microsoft Word documents

  bioinformaticssynthetic-biologymolecular-biology+ 2dna-sequencescomputer-aided-design

  Python

  •

  MIT License

  •3•32•0•0•Updated Apr 10, 2023Apr 10, 2023

• CUBA

  Public
  🏖️ The EGF Collection of Useful Bio Apps - Web demos of EGF software

  vuejsdjangoweb-development+ 4docker-composesynthetic-biologydna-assemblysequence-design

  Vue

  •

  MIT License

  •3•20•3•24•Updated Dec 10, 2022Dec 10, 2022

• DnaWeaver-online

  Public
  A web app for DNA Weaver

  Vue

  •

  Other

  •0•2•0•31•Updated Dec 8, 2022Dec 8, 2022

• egf-codons-website

  Public
  📚 Sources of the EGF Codons website, written with Vue.js

  Vue

  •0•2•0•11•Updated Dec 7, 2022Dec 7, 2022

• genome_collector

  Public
  🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

  pythonbioinformaticssynthetic-biology+ 5blasttaxidncbibowtiesynbio

  Python

  •

  Other

  •0•21•0•0•Updated Sep 30, 2022Sep 30, 2022

• OT2Metclo

  Public
  MSc project

  Python

  •0•2•1•0•Updated Aug 16, 2022Aug 16, 2022

• EGF_Docker_Jupyter

  Public
  Docker Jupyter images with (almost) all EGF packages

  Dockerfile

  •

  MIT License

  •2•1•0•0•Updated Aug 8, 2022Aug 8, 2022