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The Top 218 Genome Open Source Projects on Github

Categories > Science > Genome
Iamdinosaur ⭐ 2,760
🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus
Deepvariant ⭐ 2,339
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Gatk ⭐ 1,101
Official code repository for GATK versions 4 and up
Ai Programmer ⭐ 965
Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149
Mosdepth ⭐ 415
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Genomepy ⭐ 230
genes and genomes at your fingertips
Abyss ⭐ 227
🔬 Assemble large genomes using short reads
Karyoploter ⭐ 211
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Genometools ⭐ 203
GenomeTools genome analysis system.
Ribbon ⭐ 195
A genome browser that shows long reads and complex variants better
Soapdenovo2 ⭐ 156
Next generation sequencing reads de novo assembler.
Augustus ⭐ 148
Genome annotation with AUGUSTUS
Biomartr ⭐ 144
Genomic Data Retrieval with R
Masurca ⭐ 140
Dnabert ⭐ 133
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Viral Ngs ⭐ 129
Viral genomics analysis pipelines
Nanosim ⭐ 116
Nanopore sequence read simulator
Variantspark ⭐ 104
machine learning for genomic variants
Plyranges ⭐ 103
A grammar of genomic data transformation
Nextpolish ⭐ 95
Fast and accurately polish the genome generated by long reads.
Pyfastx ⭐ 84
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Pufferfish ⭐ 83
An efficient index for the colored, compacted, de Bruijn graph
Arv ⭐ 75
A fast 23andMe DNA parser and inferrer for Python
Arcs ⭐ 69
🌈Scaffold genome sequence assemblies using linked read sequencing data
Valr ⭐ 67
Genome Interval Arithmetic in R
Dgenies ⭐ 64
Dotplot large Genomes in an Interactive, Efficient and Simple way
Eager ⭐ 55
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Helen ⭐ 52
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
Osgenome ⭐ 50
An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies
Catch ⭐ 45
A package for designing compact and comprehensive capture probe sets.
Reveal ⭐ 39
Graph based multi genome aligner
Gnomad_methods ⭐ 36
Hail helper functions for the gnomAD project and Translational Genomics Group
Shinychromosome ⭐ 32
an R/Shiny application for interactive creation of non-circular plots of whole genomes
Panoptes ⭐ 32
Eyes on your (genomic) data
Jgi Query ⭐ 31
A simple command-line tool to download data from Joint Genome Institute databases
Metacache ⭐ 30
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Bigsdb ⭐ 29
Bacterial Isolate Genome Sequence Database (BIGSdb) - A platform for gene-by-gene bacterial population annotation and analysis.
Genomegraphs.jl ⭐ 29
A modern genomics framework for julia
Pblat ⭐ 26
parallelized blat with multi-threads support
Edge ⭐ 26
Efficiently keep track of changes to genomes
16gt ⭐ 26
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Igenomics ⭐ 26
The first app for Mobile DNA Sequence Alignment and Analysis
Ltrpred ⭐ 25
De novo annotation of young and intact retrotransposons
Tadkit ⭐ 23
3D Genome Browser
Perf ⭐ 22
PERF is an Exhaustive Repeat Finder
Gssplayground ⭐ 21
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature
Pga ⭐ 19
Plastid Genome Annotator
Companion ⭐ 19
Pipeline for automatic eukaryotic parasite annotation
Synnet Pipeline ⭐ 19
Workflow for Building Microsynteny Networks
Genome ⭐ 17
My genomic data
Mumandco ⭐ 17
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
Assembler Components ⭐ 17
Components of genome sequence assembly tools
Genomeanalysismodule ⭐ 17
Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
Scaff10x ⭐ 15
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Semantic ⭐ 15
SuperPhy for the semantic web
Corda ⭐ 14
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Chromeqc ⭐ 13
ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads
Chromeister ⭐ 13
A dotplot generator for large chromosomes
Swiftortho ⭐ 13
A high performance tool to identify orthologs and paralogs across genomes.
Dchic ⭐ 12
dcHiC: Differential compartment analysis for Hi-C datasets
Dna Sequence Machine Learning ⭐ 12
Understand DNA structure and how machine learning can be used to work with DNA sequence data.
Pyscaf ⭐ 12
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
Biobtree ⭐ 12
A bioinformatics tool to search/map identifiers, attiributes and keywords
Neat Python ⭐ 11
Genetic learning algorithm implementation for simulations, games, or general machine learning problems
Genome Fingerprints ⭐ 11
Software for creating and comparing genome fingerprints.
Pyrcos ⭐ 11
Python wrapper for Circos
Positive Selection ⭐ 10
Scripts and procedures for detecting positively selected genes and codons in primates
Bam Analysis Kit ⭐ 10
Mgse ⭐ 10
Mapping-based Genome Size Estimation
Hammlet ⭐ 10
Fast Bayesian Hidden Markov Model with Wavelet Compression
Pyrodigal ⭐ 9
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
Biogrinder ⭐ 9
Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
Transit ⭐ 9
Repository for the TRANSIT and TPP tools developed by the Ioerger Lab
Methylstar ⭐ 9
METHYLSTAR Project
Genome Blender ⭐ 9
Scripts to create cartoons of 3D genomes
Modular Assembly Hs18 ⭐ 9
Mix and match modular genome assembler components
Get_jgi_genomes ⭐ 8
A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.
Kvasir ⭐ 8
Searching for Horizontal Gene Transfer
Plethora ⭐ 8
Copy number estimation of highly duplicated sequences
Dibella.2d ⭐ 8
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
Hic Inspector ⭐ 8
HiC-inspector, a bioinformatics pipeline to facilitate the analysis of HiC dataset.
Tabsat ⭐ 8
Targeted Amplicon Bisulfite Sequencing Analysis Tool
Ipat ⭐ 7
iPat allows you to perform GWAS and GS with drags and clicks!
Parallellastz ⭐ 7
parallelLastz: Running Lastz in parallel
Setu ⭐ 7
SARS-CoV-2 Genome Assembler
Amplicon_coverage_plot ⭐ 7
interactive barplot for amplicon sequencing
Ebola On Ethereum ⭐ 7
This is a smart contract on the Ethereum blockchain that delivers a URL to a text file of the the ebola virus genome hosted on Swarm (decentralized storage).
Pecaller ⭐ 7
map and call next generation genomic sequencing
Mfannot ⭐ 7
MFannot is a program for the annotation of mitochondrial and plastid genomes
Bcfr ⭐ 6
Bin-map Constructer For RILs
Hmep ⭐ 6
Haskell Multi Expression Programming implemented with the focus on speed
Uniprot Genome Annotations Hg19 ⭐ 6
UniProt genome annotation data in hg19/GRCh37 coordinates
Tripal_jbrowse ⭐ 6
Drupal/Tripal: Drupal integration for GMOD JBrowse instances.
Addtag Project ⭐ 6
CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.
Corticall ⭐ 6
Germline DNM caller based on LdBG assembly of pathogens
Rmahunter ⭐ 6
Bacterial_wgs_training ⭐ 6
In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.
Virmet ⭐ 6
Set of tools for viral metagenomics.
Hapo G ⭐ 6
Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.
1-100 of 218 projects

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Advertising 📦 9
All Projects
Application Programming Interfaces 📦 120
Applications 📦 181
Artificial Intelligence 📦 72
Blockchain 📦 70
Build Tools 📦 111
Cloud Computing 📦 79
Code Quality 📦 28
Collaboration 📦 30
Command Line Interface 📦 48
Community 📦 81
Companies 📦 60
Compilers 📦 60
Computer Science 📦 74
Configuration Management 📦 39
Content Management 📦 167
Control Flow 📦 197
Data Formats 📦 77
Data Processing 📦 266
Data Storage 📦 132
Economics 📦 60
Frameworks 📦 198
Games 📦 122
Graphics 📦 103
Hardware 📦 148
Integrated Development Environments 📦 47
Learning Resources 📦 147
Legal 📦 28
Libraries 📦 119
Lists Of Projects 📦 21
Machine Learning 📦 336
Mapping 📦 61
Marketing 📦 15
Mathematics 📦 55
Media 📦 228
Messaging 📦 97
Networking 📦 304
Operating Systems 📦 84
Operations 📦 120
Package Managers 📦 52
Programming Languages 📦 229
Runtime Environments 📦 96
Science 📦 42
Security 📦 375
Social Media 📦 26
Software Architecture 📦 70
Software Development 📦 68
Software Performance 📦 57
Software Quality 📦 127
Text Editors 📦 45
Text Processing 📦 131
User Interface 📦 310
User Interface Components 📦 465
Version Control 📦 29
Virtualization 📦 68
Web Browsers 📦 38
Web Servers 📦 25
Web User Interface 📦 194
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