Projects in Awesome Lists tagged with dna

https://github.com/biopython/biopython

Official git repository for Biopython (originally converted from CVS)

bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment

Last synced: 13 May 2025

https://github.com/google/deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

bioinformatics deep-learning deep-neural-network deepvariant dna genome genomics machine-learning ngs science sequencing tensorflow

Last synced: 13 May 2025

https://github.com/broadinstitute/gatk

Official code repository for GATK versions 4 and up

bioinformatics dna gatk genome genomics ngs science sequencing spark

Last synced: 14 May 2025

https://github.com/galaxyproject/galaxy

Data intensive science for everyone.

bioinformatics dna genomics hacktoberfest ngs pipeline science sequencing usegalaxy workflow workflow-engine

Last synced: 11 May 2025

https://github.com/vgteam/vg

tools for working with genome variation graphs

dna genome-graph genomics graph variation-graph

Last synced: 09 Feb 2026

https://github.com/google/nucleus

Python and C++ code for reading and writing genomics data.

bioinformatics dna genomics tensorflow

Last synced: 30 Sep 2025

https://github.com/dib-lab/khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

bioinformatics bloom-filter count-min-sketch dna graph-traversal k-mer python

Last synced: 19 Jan 2026

https://github.com/bebop/poly

A Go package for engineering organisms.

alignment bioengineering bioinformatics codon-optimizer computational-biology dna dna-barcode dna-barcoding fasta genbank genetic-engineering go golden-gate mash molecular-biology plasmids primer-design sequence-hashing synbio synthetic-biology

Last synced: 11 Mar 2026

https://github.com/instadeepai/nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

deep-learning dna genomics language-model nucleotide transformer

Last synced: 03 Nov 2025

https://github.com/rosettacommons/pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

dna google-colab jupyter-notebook protein-design protein-docking protein-folding protein-structure-prediction pyrosetta rna-structure-prediction rosetta

Last synced: 12 Apr 2025

https://github.com/pallada-92/dna-3d-engine

3d engine implementation in DNA code!

3d 3d-engine biology chemical-kinetics chemical-reaction-networks chemical-reactions cube dna in-vitro molecular-biology molecular-programming piperine raymarching real-reactive-programming strand-displacement

Last synced: 16 Apr 2025

https://github.com/mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

bgzf bioinformatics dna fasta genomics indexing protein python samtools

Last synced: 14 May 2025

https://github.com/MAGICS-LAB/DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

covid dataset dna dna-processing dna-training genome genome-analysis language-model promoter promoter-analysis promoters splice splice-site transcription-factor-binding transcription-factor-binding-site transcription-factors

Last synced: 09 Oct 2025

https://github.com/FelixKrueger/Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bioinformatics dna methylation

Last synced: 30 Mar 2025

https://github.com/SupportIntelligence/Icewater

16,432 Free Yara rules created by

cluster dna malware-analysis threat yara

Last synced: 05 May 2025

https://github.com/supportintelligence/icewater

16,432 Free Yara rules created by

cluster dna malware-analysis threat yara

Last synced: 02 Apr 2025

https://github.com/lattice-automation/seqviz

a JavaScript DNA, RNA, and protein sequence viewer

biology dna igem plasmid protein rna synthetic-biology vector

Last synced: 03 Apr 2026

https://github.com/google/deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

bioinformatics deep-learning deepsomatic dna genome genomics machine science sequencing somatic-mutations somatic-variants

Last synced: 06 Mar 2026

https://github.com/Lattice-Automation/seqviz

a JavaScript DNA, RNA, and protein sequence viewer

biology dna igem plasmid protein rna synthetic-biology vector

Last synced: 03 Dec 2025

https://github.com/samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 14 May 2025

https://github.com/lmdu/pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

assembly bioinformatics biology dna fasta fastq genome python sequence

Last synced: 15 May 2025

https://github.com/chanzuckerberg/shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

assembly de-novo dna long-read nanopore pacbio sequencing

Last synced: 05 May 2025

https://github.com/songlab-cal/gpn

Genomic Pre-trained Network

dna genomics language-model variant-effect-prediction

Last synced: 07 May 2025

https://github.com/nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

clade clades coronavirus covid covid-19 covid19 dna influenza ncov neherlab next-generation-sequencing nextstrain research rna sars-cov-2 science sequences sequencing strain virus

Last synced: 15 Apr 2026

https://github.com/igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

bioinformatics dna fast5 fasta fastq genomics gtf illumina nanopore science sequencing vcf workflow

Last synced: 21 Jan 2026

https://github.com/ratschlab/metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

alignment assembly dna graph metagenomics search

Last synced: 15 Jan 2026

https://github.com/ugeneunipro/ugene

UGENE is free open-source cross-platform bioinformatics software

bioinformatics cpp cross-platform dna msa ngs pipeline qt5 science sequencing ugene workflow

Last synced: 04 Mar 2026

https://github.com/pydna-group/pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

anaconda assembly-strategies bioinformatics biology biopython cloning-strategies dna fasta gel gel-electrophoresis gel-simulation genbank gibson-assembly jupyter jupyter-notebook jupyter-notebooks pydna python simulation

Last synced: 06 Feb 2026

https://github.com/bowang-lab/bioreason

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model

bioinformatics computational-biology dna foundation-models grpo large-language-models reasoning

Last synced: 12 Jun 2025

https://github.com/marrink-lab/polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

atomistic-simulations carbohydrates coarse-graining dna hacktoberfest macromolecules martini md polymers

Last synced: 12 Apr 2025

https://github.com/elkimek/get-based

Private, local-first health intelligence for labs, 51 curated SNPs, wearables, light exposure, Biology Scores, optional AI, encrypted sync, sharing, and Agent Access.

ai biomarker-tracking biomarkers blood-test blood-work dashboard dna evidence-based free genetics health health-dashboard lab-results local-first open-source pdf-import privacy-first pwa self-hosted snp

Last synced: 27 Aug 2026

https://github.com/cslarsen/arv

A fast 23andMe DNA parser and inferrer for Python

23andme bioinformatics dna genome python snpedia snps

Last synced: 20 Aug 2025

https://github.com/apriha/snps

tools for reading, writing, generating, merging, and remapping SNPs

bioinformatics chromosomes dna snps vcf

Last synced: 28 Jan 2026

https://github.com/kennethreitz/context

Raw dump of Kenneth Reitz's DNA Sequence, Ancestry, Genealogy, &c.

23andme ancestry dna gedcom gedcom-files geneology genome human-genome kennethreitz promethease

Last synced: 31 Jan 2026

https://github.com/urmi-21/orfipy

Fast and flexible ORF finder

bioinformatics codon-tables dna extract-orfs orf-detection orf-finder orf-search protein python

Last synced: 13 Dec 2025

https://github.com/igordot/sns

Analysis pipelines for genomic sequencing data

analysis atac-seq bioinformatics dna genomics illumina nyu pipeline rna-seq rrbs sequencing wes wgbs wgs

Last synced: 21 Jan 2026

https://github.com/cslarsen/dna-traits

A fast 23andMe genome text file parser, now superseded by arv

23andme bioinformatics dna genomics health-report python snpedia snps

Last synced: 19 Jul 2025

https://github.com/MAGICS-LAB/DNABERT_S

DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models

dna dna-embedding embedding

Last synced: 15 Aug 2025

https://github.com/danielbiegler/visualize-dna-sequences

Visualizing DNA Sequences via Javascript

bootstrap bootstrap4 canvas dna html html5 javascript sequence visual visualization visualizing visualizing-dna-sequences

Last synced: 19 Jul 2025

https://github.com/jvrana/benchling-api

A python wrapper for the benchling api

api-wrapper dna dna-sequences

Last synced: 16 Jan 2026

https://github.com/IQTLabs/squiggle

📈 DNA Sequence Visualization for Humans

dna visualization

Last synced: 05 May 2025

https://github.com/broadinstitute/adapt

A package for designing activity-informed nucleic acid diagnostics for viruses.

bioinformatics diagnostics dna genomics science viral

Last synced: 10 Oct 2025

https://github.com/qdata/chromegcn

Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

dna dna-sequences genomics graph-convolutional-networks graph-neural-networks hi-c

Last synced: 14 Mar 2026

https://github.com/0x77dev/dna

It's quite fascinating - I fit into a 17.6 MB text file, or at least part of me does*

23andme dna

Last synced: 07 Mar 2026

https://github.com/liberu-genealogy/php-dna

DNA processing and manipulating for PHP 8.3

dna dna-processing laravel laravel10 php php8

Last synced: 11 Apr 2025

https://github.com/brandonsaldan/codex

A minimal genetic data explorer that processes all genetic information locally.

bioinformatics dna genetics genome-analysis snpedia

Last synced: 27 Dec 2025

https://github.com/fomightez/sequencework

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics list lists protein-sequences python rna

Last synced: 12 Apr 2025

https://github.com/n-szulc/fingernat

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

bioinformatics bioinformatics-tool dna drug-target-interactions interactions ligand-complex ligand-receptor-interaction ligand-target molecular-interactions nucleic-acids rna rna-ligand-complexes scientific-computing structural-bioinformatics structural-interaction-fingerprint

Last synced: 26 Oct 2025

https://github.com/statgenlmu/coala

A Framework for Coalescent Simulation in R

coalescent dna evolution popgen rstats simulation

Last synced: 21 Feb 2026

https://github.com/opendnd/genetica

This is a tool for using a simplified genetics system to generate inheritable traits for DnD characters.

chromosome dm-tools dna dnd dnd-characters dnd-npc-generator dnd-tools dnd5e dungeon-master dungeons-and-dragons inheritable-traits roll simplified-genetics trait

Last synced: 24 Apr 2025

https://github.com/karma9874/dna-cipher-script-ctf

A simple script to decode the genome DNA binary sequence (CTF Challenge)

binary cipher ctf dna

Last synced: 09 Apr 2025

https://github.com/eyss/h-wiki-back

DNA code for H-Wiki, a holochain-powered wiki for groups and communities

dapp decentralized dna happ holochain wiki

Last synced: 12 May 2025

https://github.com/kloetzl/libdna

♥ Essential Functions for DNA Manipulation

bioinformatics dna simd-optimizations

Last synced: 18 Jan 2026

https://github.com/tzok/eltetrado

A Python application to find and classify tetrads and quadruplexes in DNA/RNA 3D structures

bioinformatics dna nucleic-acids quadruplexes rna visualization

Last synced: 08 Apr 2026

https://github.com/edinburgh-genome-foundry/bandwagon

🎺 Plot DNA digestion band patterns with Python

agarose-gel dna molecular-biology plotting synthetic-biology

Last synced: 15 Jul 2025

https://github.com/paulsengroup/modle

High-performance stochastic modeling of DNA loop extrusion interactions

bioinformatics biology cpp cpp17 dna hic high-performance loop-extrusion stochastic-model tad topologically-associated-domains

Last synced: 16 Jan 2026

https://github.com/cabb99/open3spn2

An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM

dna forcefield openmm

Last synced: 16 Jan 2026

https://github.com/devinus/genome

My genomic data

dna dna-data genome

Last synced: 05 Feb 2026

https://github.com/feliixx/gotranseq

convert nucleic sequence in protein sequence

bioinformatics dna go protein-sequences translation

Last synced: 30 Apr 2025

https://github.com/chgibb/PHAT

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

alignment analysis bam bam-files bioinformatics bioinformatics-analysis bioinformatics-tool circos circos-graphs circos-plot dna electron host next-generation-sequencing ngs pathogen phat quality-control snps visualization

Last synced: 05 May 2025

https://github.com/zyxue/biogrinder

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

amplicon-datasets amplicon-library biogrinder dna genome grinder shotgun simulated-datasets simulation

Last synced: 07 May 2025

https://github.com/jvrana/primer3-py-plus

A easy-to-use Python API for Primer3 primer design.

biocad biodesign dna molecular-biology

Last synced: 14 Jan 2026

https://github.com/jumitti/tfinder

Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.

api dna dna-sequences iupac jaspar ncbi promoter-sequences python python3 responsive-elements streamlit terminator-sequences transcription-factor transcription-factor-binding-site transcription-factors webtools

Last synced: 11 Apr 2025

https://github.com/prihoda/usum

USUM: Plotting sequence similarity using USEARCH & UMAP & t-SNE

dna plot protein sequence similarity t-sne uclust umap usearch

Last synced: 09 Sep 2025

https://github.com/HelixGenomics/Genomic-Agent-Discovery

AI agents that collaborate to analyze your DNA. 12 public databases, real-time dashboard, runs 100% locally. Drop in your 23andMe, AncestryDNA, or VCF file.

23andme ai-agents ancestrydna bioinformatics claude clinvar dna genetic-testing genomics gwas llm mcp model-context-protocol multi-agent personal-genomics pharmacogenomics precision-medicine privacy snp vcf

Last synced: 19 Apr 2026

https://github.com/const-ae/neural_network_dna_demo

Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction

demo dna ipython neural-network

Last synced: 09 Apr 2025

https://github.com/rajatdiptabiswas/dna-compression

🧬 Analyzing compression algorithms for genomic sequencing data

bioinformatics compression dna dynamic-markov-compression research

Last synced: 12 Jul 2025

https://github.com/dib-lab/rcgrep

Search text files for DNA sequences and their reverse complements

bioinformatics dna genomics search

Last synced: 19 Jan 2026

https://github.com/helixgenomics/genomic-agent-discovery

AI agents that collaborate to analyze your DNA. 12 public databases, real-time dashboard, runs 100% locally. Drop in your 23andMe, AncestryDNA, or VCF file.

23andme ai-agents ancestrydna bioinformatics claude clinvar dna genetic-testing genomics gwas llm mcp model-context-protocol multi-agent personal-genomics pharmacogenomics precision-medicine privacy snp vcf

Last synced: 05 Apr 2026

https://github.com/cgevans/qslib

QSLib is a package for interacting with Applied Biosystems' QuantStudio qPCR machines, intended for non-qPCR uses, such as DNA computing and molecular programming systems.

dna molecular-computing python

Last synced: 28 Dec 2025

https://github.com/smsaladi/codonw-slim

A slimmed down fork of CodonW with python bindings

bioinformatics codon-usage dna protein python-binding

Last synced: 04 Apr 2026

https://github.com/soedinglab/peng-motif

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.

bioinformatics chip-seq dna motif-discovery rna

Last synced: 27 Apr 2025

https://github.com/henrikbengtsson/aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

affymetrix analysis copy-number dna expression hpc large-scale microarray notebook package r reproducibility rna

Last synced: 10 Apr 2025

https://github.com/bvu-bilsab/dima

A command-line tool that analyses the diversity and motifs of protein/nucleotide sequences.

bioinformatics biology dna protein python research rna rust virus

Last synced: 22 Apr 2025

https://github.com/fischuu/snakebite-holoruminant-metag

Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators

dna metagenome-assembled-genomes metagenomics snakemake snakemake-workflow

Last synced: 18 Feb 2026

https://github.com/gagniuc/visual-sequence-alignment-in-vb6

This highly visual and responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time.

dna dna-sequences gap genetics genomics global heatmap match matrix mismatch proteomics rna score sequence-alignment traceback visualization

Last synced: 06 Mar 2026

https://github.com/antonoresten/vectorizedkmers.jl

Fast K-mer counting in Julia

dna kmer sequence

Last synced: 11 Dec 2025

https://github.com/robertcsapo/cisco-dnac-platform-webex-notifications

Receive Events from Cisco DNA Center and push the information to Cisco Webex Teams

cisco cisco-dna-center cisco-webex-teams dna dna-center dnac docker docker-compose flask python python-webhook receive-events webex webhook

Last synced: 04 Sep 2025

https://github.com/thecoderpinar/nanodna-nanorobot-simulation

nanoDNA-nanoROBOT-simulation: Open-source Python project for modeling and simulating DNA-based nanorobot behavior. 🧬🤖

algorithms artificial-intelligence bioengineering bioinformatics biomedical-engineering computational-biology computational-modeling data-analysis dna machine-learning molecular-biology nanotechnology neural-networks open-source python science simulation

Last synced: 30 Apr 2025

https://github.com/biojulia/biomarkovchains.jl

Representing biological sequences as Markov chains

bioinformatics biology dna julia julialang markov-chain

Last synced: 11 Dec 2025

https://github.com/BioJulia/BioMarkovChains.jl

Representing biological sequences as Markov chains

bioinformatics biology dna julia julialang markov-chain

Last synced: 17 Aug 2025

https://github.com/brentp/falas

Fragment-Aware Local Assembly for Short-reads

assembly dna genomics structural-variation

Last synced: 29 Oct 2025

https://github.com/cobilab/jarvis3

Efficient compression of biological data

data-compression dna dna-sequences

Last synced: 21 Apr 2026

https://github.com/fomightez/blast-binder

Repo for running command line-based BLAST in Jupyter environment provided via Binder.

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics pandas pandas-dataframe protein-sequences python rna

Last synced: 14 Jul 2025

https://github.com/hdg204/Rdna-nexus

Functions to analyse UK Biobank genetic data directly from DNA Nexus' RStudio Workbench

biobank bioinformatics dna genetics nexus r risk scores snp uk

Last synced: 09 Apr 2025

https://github.com/gear-genomics/sabre

Sequence Alignment Browser

alignment dna gear-genomics genomics research sequence visualization

Last synced: 17 Jan 2026

https://github.com/sam-k/seq-quality-trimming

Trimming Sanger sequencing reads by quality

dna genomics metabarcoding sequencing ta-cloning

Last synced: 19 Apr 2025

https://github.com/bioinformaticsfmrp/bioc2017.tcgabiolinks.elmer

Integrative analysis workshop with TCGAbiolinks and ELMER

bioc2017 bioconductor dna gdc regulatory-network tcga tcgabiolinks

Last synced: 24 Jan 2026

https://github.com/deepstupid/genocoin

For all Debts, Public and Genetic - BloodChain Reference Implementation - The antihuman genome project

banking biohacking bitcoin cancer cryptography debt dna eugenics euthanasia finance genetic genome investment money mutations psychopathy slavery

Last synced: 20 Mar 2025

https://github.com/edmundkorley/text2dna

A small service to encode input as a DNA sequence 🐛

bioinformatics dna encoding storage

Last synced: 22 Apr 2025

https://github.com/biomedsciai/geno4sd

An python omics data toolkit for the analysis across biological scales

cancer-genomics dna machine-learning omics omics-data population-genetics population-genomics

Last synced: 28 Jul 2025

https://github.com/mbelmadani/motifgp

Motif discovery for DNA sequences using multiobjective optimization and genetic programming.

bioinformatics chip-seq deap dna dna-sequences genetic-programming jaspar motif motif-discovery multiobjective-optimization network-expressions nsga-ii pareto-front python regular-expressions sequences strongly-typed transcription-factor-binding transcription-factors

Last synced: 07 Jul 2025

https://github.com/jangevaare/geneticbitarrays.jl

BitArray representation of genetic sequences in Julia

bioinformatics dna genetic-sequences julia rna

Last synced: 22 Apr 2025

https://github.com/karrlab/bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

crosslinks dna dna-damage epigenetics methylation phosphorylation post-transcriptional-regulation post-translational-modification protein proteoform rna

Last synced: 25 Jun 2025

https://github.com/gregorybchris/typogenetics

From Douglas Hofstadter's "Gödel, Escher, Bach" (1979)

biology dna douglas genetics hofstadter replication rna science strands typogenetics

Last synced: 30 Aug 2025

https://github.com/gagniuc/sequence-logo-relative-style

Sequence Logo - relative style is an alternative that provides full control over how the graphics of a Sequence Logo should look like, and is an alternative to an application called WebLogo. All the inner workings of this open source application are written in native javascript.

dna dna-processing html-css-javascript html5 html5-canvas javascript js motif proteomics rna-sequences sequence-logo