Repositories list

• Sequeduct_demo

  Public
  Demonstration data for the Sequeduct pipeline

  HTML

  •1•5•0•0•Updated Dec 12, 2025Dec 12, 2025

• Sequeduct

  Public
  Sequencing analysis pipeline

  Nextflow

  •

  GNU General Public License v3.0

  •0•15•1•0•Updated Dec 12, 2025Dec 12, 2025

• Geneblocks

  Public
  :diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

  pythonsynthetic-biologysequence-analysis

  Python

  •

  MIT License

  •3•42•0•0•Updated Nov 5, 2025Nov 5, 2025

• DnaChisel

  Public
  :pencil2: A versatile DNA sequence optimizer

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

  Python

  •

  MIT License

  •50•262•15•3•Updated Nov 5, 2025Nov 5, 2025

• Sequensign

  Public
  Handling digital signatures in sequence files

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 24, 2025Sep 24, 2025

• Examples

  Public

  Edinburgh-Genome-Foundry/Examples’s past year of commit activity
  Collection of Python modules and Jupyter notebook examples

  HTML

  •

  MIT License

  •2•7•0•0•Updated Jul 3, 2025Jul 3, 2025

• DnaFeaturesViewer

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

  visualizationbioinformaticssynthetic-biology+ 3genbankmolecular-biologydna-visualization

  Python

  •

  MIT License

  •104•681•33•3•Updated Jul 2, 2025Jul 2, 2025

• biofoundry_workflows

  Public
  biofoundry workflows

  CSS

  •

  Other

  •3•0•0•0•Updated Jun 20, 2025Jun 20, 2025

• EGF_Docker_Jupyter

  Public
  Docker Jupyter images with (almost) all EGF packages

  Dockerfile

  •

  MIT License

  •1•1•0•0•Updated Jun 12, 2025Jun 12, 2025

• BandWitch

  Public
  💫 Computer-aided DNA assembly validation and identification from restriction digests.

  synthetic-biologyexperimental-designdna-assembly+ 1fragment-analysis

  Python

  •

  MIT License

  •0•15•0•0•Updated May 29, 2025May 29, 2025

• Plateo

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

  parsersynthetic-biologylab-automation

  Python

  •

  MIT License

  •7•46•2•0•Updated May 29, 2025May 29, 2025

• Sequeduct_Methyl

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 28, 2025May 28, 2025

• Sequeduct_Methyl_archive

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated May 26, 2025May 26, 2025

• Sequeduct_Methyl_demo

  Public
  Demonstration data for the Sequeduct Methyl pipeline

  0•0•0•0•Updated May 26, 2025May 26, 2025

• Overhang

  Public
  Compendium of overhangs

  Python

  •

  MIT License

  •1•3•0•0•Updated May 15, 2025May 15, 2025

• Minotaor

  Public
  An amino acid sequence annotator

  Python

  •

  MIT License

  •1•17•0•0•Updated May 15, 2025May 15, 2025

• tatapov

  Public
  :paw_prints: DNA overhang misannealing data for Python

  synthetic-biologydna-assemblygolden-gate+ 1dna-design

  Python

  •

  MIT License

  •1•13•0•0•Updated May 15, 2025May 15, 2025

• Seq_Report

  Public
  Simple reporting on a set of sequences for documentation purposes

  Python

  •

  MIT License

  •0•1•0•0•Updated May 12, 2025May 12, 2025

• BandWagon

  Public
  🎺 Plot DNA digestion band patterns with Python

  synthetic-biologydnaplotting+ 2molecular-biologyagarose-gel

  Python

  •

  MIT License

  •3•20•1•0•Updated May 12, 2025May 12, 2025

• genedom

  Public
  Batch domestication of genetic parts with Python

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

  Python

  •

  MIT License

  •1•16•0•0•Updated May 12, 2025May 12, 2025

• DnaWeaver

  Public
  A route planner for DNA assembly

  synthetic-biologyplanningdna-assembly+ 1cloning-strategy

  Python

  •

  MIT License

  •9•36•8•0•Updated May 12, 2025May 12, 2025

• DnaCauldron

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

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

  Python

  •

  MIT License

  •10•66•5•0•Updated May 12, 2025May 12, 2025

• crazydoc

  Public
  Read DNA sequences from colourful Microsoft Word documents

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

  Python

  •

  MIT License

  •4•34•0•1•Updated May 12, 2025May 12, 2025

• easy_dna

  Public
  :school_satchel: Python library to read, write, edit DNA sequences

  Python

  •

  MIT License

  •1•7•0•0•Updated May 12, 2025May 12, 2025

• SnapGeneReader

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

  convertersynthetic-biologybiopython+ 3genbanksequence-designsnapgene

  Python

  •

  MIT License

  •16•29•0•0•Updated May 10, 2025May 10, 2025

• python_codon_tables

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

  bioinformaticssynbiocodon-optimization+ 1codon-usage

  Python

  •

  Creative Commons Zero v1.0 Universal

  •11•42•0•0•Updated May 9, 2025May 9, 2025

• Proglog

  Public
  :memo: Logs and progress bars manager for Python

  pythonloggerprogress-bar

  Python

  •

  MIT License

  •6•115•3•1•Updated May 9, 2025May 9, 2025

• Flametree

  Public
  :fire: Python file and zip operations made easy

  pythonfilesystemzip+ 2filearchive

  Python

  •

  MIT License

  •10•149•6•1•Updated May 9, 2025May 9, 2025

• pdf_reports

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

  pythonpdfreporting

  Python

  •

  MIT License

  •41•248•12•0•Updated May 8, 2025May 8, 2025

• sequenticon

  Public
  :space_invader: Generate identicons for DNA sequences with Python

  synthetic-biologylimsdna-sequences+ 1sequence-editing

  Python

  •

  MIT License

  •5•38•0•0•Updated May 8, 2025May 8, 2025