dna-assembly

There are 2 repositories under dna-assembly topic.

• Edinburgh-Genome-Foundry / DnaCauldron

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

  synthetic-biologymolecular-biologydna-assemblygolden-gatecloning-simulator
  Language:Python 49

• Edinburgh-Genome-Foundry / Primavera

  :cherry_blossom: Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.

  sequencingprimer-designdna-assemblysynthetic-biology
  Language:Python 33

• Edinburgh-Genome-Foundry / DnaWeaver

  A route planner for DNA assembly

  synthetic-biologydna-assemblycloning-strategyplanning
  Language:Python 28

• Edinburgh-Genome-Foundry / Caravagene

  🎨 Python library to plot multi-part genetic constructs

  synthetic-biologymolecular-biologysequence-designdna-assembly
  Language:Python 24

• Lattice-Automation / primers

  A PCR primer tool for DNA assembly flows

  pcrprimersdna-assemblydnagibson-assemblygolden-gate-cloning
  Language:Python 24

• Edinburgh-Genome-Foundry / CUBA

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

  vuejsdjangosynthetic-biologydna-assemblysequence-designdocker-composeweb-development
  Language:Vue 19

• Lattice-Automation / synbio

  a DNA assembly library

  protocolsroboticsdna-assemblyplasmidsannotationseqrecordpicklist
  Language:Python 17

• Edinburgh-Genome-Foundry / BandWitch

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

  synthetic-biologydna-assemblyexperimental-designfragment-analysis
  Language:Python 16

• Edinburgh-Genome-Foundry / genedom

  Batch domestication of genetic parts with Python

  synbiosynthetic-biologysequence-designdna-assemblypart-domestication
  Language:Python 14

• bioinfologics / Pseudoseq.jl

  Fake genomes, fake sequencing, real insights.

  dna-sequencesgenome-assemblydna-sequencingsimulationsimulatordna-assemblypaired-endlong-readslinked-reads
  Language:Julia 13

• Edinburgh-Genome-Foundry / tatapov

  :paw_prints: DNA overhang misannealing data for Python

  golden-gatesynthetic-biologydna-assemblydna-design
  Language:Python 12

• Edinburgh-Genome-Foundry / GoldenHinges

  :link: Short overhangs design for DNA assembly

  dna-assemblysequence-designsynthetic-biology
  Language:Python 11

• czmilanna / nanoforms

  The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology. PeerJ, 2022). It is meant to be the source for standalone server installation. https://doi.org/10.7717/peerj.13056

  ngsbioinformaticsoxford-nanoporegenomicswebserverdna-sequencingdna-assemblymicrobial-genomes
  Language:JavaScript 9

• Edinburgh-Genome-Foundry / kappagate

  :crystal_ball: Predict DNA assembly clone validity rates - powered by Kappa

  synthetic-biologydna-assemblylab-automationsequence-designkappa-languagebiological-simulations
  Language:Python 9

• Edinburgh-Genome-Foundry / zymp

  :scissors: Design compact restriction sites arrays (python utility)

  dna-assemblysequence-designrestriction-sitessynthetic-biology
  Language:Python 9

• Edinburgh-Genome-Foundry / dab

  :point_right: EGF Design and Build, the Foundry's DNA design ordering portal

  dna-designsynthetic-biologydna-assemblygenome-foundry
  Language:Vue 8

• Edinburgh-Genome-Foundry / egf-shared-documents

  :books: Shared slideshows, courses, etc. from the EGF

  synthetic-biologydna-assemblydna-foundry
  Language:HTML 8

• JBEI / dnada

  DNAda is a web application that integrates the J5 DNA assembly software with robotic liquid handlers

  automationdna-assemblysynthetic-biology
  Language:Python 8

• Edinburgh-Genome-Foundry / igem-registry-downloader

  Download the full iGEM database of parts

  synthetic-biologyigemigem-websitegenetic-partsdna-assemblyigem-apiigem-registry
  Language:Python 4

• Edinburgh-Genome-Foundry / saboteurs

  :bomb: Identify elements impairing success accross group experiments.

  lab-automationdna-assemblyquality-controldna-part
  Language:Python 4

• hmjeon / PERDIX

  Programmed Eulerian Routing for DNA Design using X-overs

  dna-origamidna-assemblynanostructuresdual-graphspanning-tree
  Language:Fortran 4

• Meristembio / Weaver

  Open source web app for DNA design and management

  biotechnologydnadna-assemblylabmanagementopen-sourcemolecular-tools
  Language:JavaScript 4

• avivace / dna-recombination

  Computer Science B.Sc thesis paper and final stage experience. Approaching a Computational Biology Problem with integer linear programming tools.

  thesis-paperthesisbachelor-thesisbachelor-projectbioinformaticscomputational-biologydna-assemblydna-rearrangementdna-recombinationciliate-speciesgurobilinear-programminginteger-linear-programming
  Language:TeX 3

• intbio-ncl / BiomationScripterLib

  A Python library to assist with scripting bio-automation protocols

  dna-assemblylaboratory-automationliquid-handlingliquid-handling-robotmolecular-biologysynthetic-biologylab-automationopentrons
  Language:Python 3

• hmjeon / METIS-pub

  Designer three layered wireframe DNA origami

  dna-origamidna-assemblynanostructuresdual-graphspanning-trees
  Language:Fortran 2

• LasVegasCoder / Data-Science

  Data Science Tools, Libraries, Classes and Functions

  data-sciencedatasciencedata-science-toolkitdata-science-toolboxdata-science-workbenchpythondnadna-sequencesdna-assemblydistance-calculationdistancedna-sequence-analysisdna-sequence-readerdna-similaritydna-translationdna-transcriptioner-generatorfind-neareast-neighborsmajority-voteword-counter
  Language:Python 2

• ZackSkeet / CELLO-DNA-Computing

  Projects written in CELLO

  biocomputingcellodnadna-assemblymolecularmolecular-biology
  2

• hmjeon / DAEDALUS2-pub

  dna-origamidna-assemblydna-sequenceswireframenanostructures
  Language:Fortran 1

• hmjeon / TALOS

  Three-dimensional, Algorithmically-generated Library of DNA Origami Shapes

  dna-origamidna-assemblynanostructuresdual-graphspanning-treesdna-sequences
  Language:Fortran 1

• ishanshukla97 / extras

  Implementation of random algorithms

  dna-assemblydna-sequencing
  Language:Jupyter Notebook 1

• jvrana / pyblast

  BLAST wrapper for python that handles circular sequences

  biologyblastdnadna-sequencesdna-assembly
  Language:Python 1

• NavpreetDevpuri / DNAc

  DNAc is a programming language for DNAs.

  dnadna-assemblydna-sequencedna-methylationdna-processinggenetic-programminggenetic-programming-algorithmgenetic-algorithmgeneticsgenetic-variantsgenetic-analysis
  1

• pablocarderam / genetargeter

  Creates a construct developed by the Niles Lab at MIT, designed to deliver a 3' UTR post-transcriptional regulatory element payload to a specific given gene in Plasmodium falciparum.

  molecular-biologymalariaplasmodiumplasmodium-falciparumdna-assemblycrisprcrispr-designbioinformatics
  Language:Python 1

• mfileman / Circular-String

  This was a project for my bioinformatics class. We studied the circular string problem and its application to bioinformatics and sequence generation / reconstruction. This project solves the circular string problem taking in an integer k, by creating a DeBruijn graph and generating a Euler cycle from it (the edges corresponding to all possible binary k-mers).

  bioinformaticscircular-stringdna-assemblyswift
  Language:Swift 0

• sblabkribb / Automated-protocol

  Automated synthetic biology protocols with ot2

  dna-assemblyliquid-handleropentrons-ot2
  Language:Python 0

• sghignone / canu

  openjdk:8 based release of CANU, a PacBio assembler

  containerdna-assemblydocker-containerdockerfilepacbio
  Language:Singularity 0