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The Top 109 Genomics Open Source Projects
Categories
>
Science
>
Genomics
Biopython
⭐
2,615
Official git repository for Biopython (originally converted from CVS)
Deepvariant
⭐
2,202
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Deep Review
⭐
1,139
A collaboratively written review paper on deep learning, genomics, and precision medicine
Gatk
⭐
988
Official code repository for GATK versions 4 and up
Bwa
⭐
955
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Minimap2
⭐
900
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Galaxy
⭐
805
Data intensive science for everyone.
Vg
⭐
706
tools for working with genome variation graphs
Hail
⭐
704
Scalable genomic data analysis.
Nucleus
⭐
656
Python and C++ code for reading and writing genomics data.
Ncbi Genome Download
⭐
489
Scripts to download genomes from the NCBI FTP servers
Deeptools
⭐
444
Tools to process and analyze deep sequencing data.
Biojava
⭐
430
📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Vcflib
⭐
412
C++ library and cmdline tools for parsing and manipulating VCF files
Goatools
⭐
409
Python library to handle Gene Ontology (GO) terms
Bwa Mem2
⭐
400
The next version of bwa-mem
Jcvi
⭐
399
Python library to facilitate genome assembly, annotation, and comparative genomics
Jbrowse
⭐
392
A modern genome browser built with JavaScript and HTML5.
Bowtie2
⭐
362
A fast and sensitive gapped read aligner
Megahit
⭐
340
Ultra-fast and memory-efficient (meta-)genome assembler
Jvarkit
⭐
310
Java utilities for Bioinformatics
Pyfaidx
⭐
307
Efficient pythonic random access to fasta subsequences
Gwa_tutorial
⭐
291
A comprehensive tutorial about GWAS and PRS
Arvados
⭐
273
An open source platform for managing and analyzing biomedical big data
Seq
⭐
262
A high-performance, Pythonic language for bioinformatics
Pygeno
⭐
259
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Vcfanno
⭐
258
annotate a VCF with other VCFs/BEDs/tabixed files
Bio.jl
⭐
257
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
Postgui
⭐
252
A React web application to query and share any PostgreSQL database.
Eggnog Mapper
⭐
251
Fast genome-wide functional annotation through orthology assignment
Hap.py
⭐
247
Haplotype VCF comparison tools
Canvasxpress
⭐
247
JavaScript VisualizationTools
Cyvcf2
⭐
242
cython + htslib == fast VCF and BCF processing
Dragonn
⭐
222
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
Bowtie
⭐
221
An ultrafast memory-efficient short read aligner
Htsjdk
⭐
218
A Java API for high-throughput sequencing data (HTS) formats.
Miniasm
⭐
216
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Pyranges
⭐
215
Performant Pythonic GenomicRanges
Bedops
⭐
214
🔬 BEDOPS: high-performance genomic feature operations
Genomeworks
⭐
211
SDK for GPU accelerated genome assembly and analysis
Flowcraft
⭐
206
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Minigraph
⭐
205
Proof-of-concept seq-to-graph mapper and graph generator
Juicer
⭐
200
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Higlass
⭐
199
Fast large scale matrix visualization for the web.
Sequenceserver
⭐
196
Intuitive local web frontend for the BLAST bioinformatics tool
Intermine
⭐
193
A powerful open source data warehouse system
Genometools
⭐
184
GenomeTools genome analysis system.
Ideogram
⭐
181
Chromosome visualization for the web
Ribbon
⭐
181
A genome browser that shows long reads and complex variants better
Deep Rules
⭐
179
Ten Quick Tips for Deep Learning in Biology
Wgsim
⭐
175
Reads simulator
Goleft
⭐
175
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Roary
⭐
174
Rapid large-scale prokaryote pan genome analysis
Janggu
⭐
167
Deep learning infrastructure for bioinformatics
Glow
⭐
159
An open-source toolkit for large-scale genomic analysis
Viral Ngs
⭐
149
Viral genomics analysis pipelines
Vcfr
⭐
148
Tools to work with variant call format files
Smoove
⭐
146
structural variant calling and genotyping with existing tools, but, smoothly.
Biomartr
⭐
144
Genomic Data Retrieval with R
Awesome Bioinformatics Benchmarks
⭐
138
A curated list of bioinformatics bench-marking papers and resources.
Hgvs
⭐
137
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Artemis
⭐
135
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Hts Nim
⭐
131
nim wrapper for htslib for parsing genomics data files
Octopus
⭐
130
Bayesian haplotype-based mutation calling
Hifiasm
⭐
128
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Miso Lims
⭐
127
MISO: An open-source LIMS for NGS sequencing centres
Somalier
⭐
127
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Benchmarking Tools
⭐
125
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Sarek
⭐
124
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Circlator
⭐
121
A tool to circularize genome assemblies
Kmer Cnt
⭐
117
Code examples of fast and simple k-mer counters for tutorial purposes
Hicexplorer
⭐
115
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Ngless
⭐
114
NGLess: NGS with less work
Qqman
⭐
113
An R package for creating Q-Q and manhattan plots from GWAS results
Cooler
⭐
110
A cool place to store your Hi-C
Slivar
⭐
110
variant expressions, annotation, and filtering for great good.
Cgranges
⭐
110
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Msprime
⭐
101
Simulate genealogical trees and genomic sequence data using population genetic models
Genomics
⭐
98
A collection of scripts and notes related to genomics and bioinformatics
Chipseq_pipeline
⭐
96
AQUAS TF and histone ChIP-seq pipeline
Ariba
⭐
95
Antimicrobial Resistance Identification By Assembly
Smudgeplot
⭐
95
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Gcp For Bioinformatics
⭐
94
GCP Essentials for Bioinformatics Researchers
Ga4gh Server
⭐
93
Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
Bio
⭐
90
Bioinformatics library for .NET
Genomicsqlite
⭐
87
Genomics Extension for SQLite
Dkm
⭐
86
Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features
Awesome 10x Genomics
⭐
82
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
Igv Snapshot Automator
⭐
81
Script to automatically create and run IGV snapshot batchscripts
Scoary
⭐
80
Pan-genome wide association studies
Svtyper
⭐
79
Bayesian genotyper for structural variants
Sibeliaz
⭐
75
A fast whole-genome aligner based on de Bruijn graphs
Fastq.bio
⭐
74
An interactive web tool for quality control of DNA sequencing data
Bgt
⭐
72
Flexible genotype query among 30,000+ samples whole-genome
Gubbins
⭐
67
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Bluegenes
⭐
66
A friendly next-generation interface for Genomic data discovery powered by InterMine
Dna Nn
⭐
59
Model and predict short DNA sequence features with neural networks
Mixomics
⭐
54
Development repository for the Bioconductor package 'mixOmics '
Aioli
⭐
50
Framework for building fast genomics web tools with WebAssembly and WebWorkers
Quota Alignment
⭐
47
Guided synteny alignment between duplicated genomes (within specified quota constraint)
1-100 of 109 projects
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📦 83
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📦 60
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📦 63
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📦 80
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📦 175
Control Flow
📦 213
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Data Processing
📦 276
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📦 135
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📦 64
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📦 215
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📦 129
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📦 110
Hardware
📦 152
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📦 49
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📦 166
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📦 29
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📦 129
Lists Of Projects
📦 22
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📦 347
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📦 64
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📦 15
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📦 55
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📦 239
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📦 98
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📦 315
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📦 89
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📦 121
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📦 55
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📦 245
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📦 42
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📦 396
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📦 27
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📦 72
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📦 72
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📦 58
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📦 133
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📦 49
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📦 136
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📦 330
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📦 514
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📦 71
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📦 42
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📦 210