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The Top 1,801 Genomics Open Source Projects

Categories > Science > Genomics
Biopython ⭐ 3,356
Official git repository for Biopython (originally converted from CVS)
dependent packages 978total releases 56most recent commit 15 hours agopypi biopython} Downloads
Deepvariant ⭐ 2,608
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
most recent commit 2 months ago
Deeplearning Biology ⭐ 1,789
A list of deep learning implementations in biology
most recent commit 6 hours ago
Seurat ⭐ 1,635
R toolkit for single cell genomics
most recent commit 6 days ago
Gatk ⭐ 1,342
Official code repository for GATK versions 4 and up
dependent packages 2total releases 44most recent commit 3 days ago
Minimap2 ⭐ 1,337
A versatile pairwise aligner for genomic and spliced nucleotide sequences
dependent packages 24total releases 25most recent commit 4 days agopypi mappy} Downloads
Bwa ⭐ 1,188
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
most recent commit 2 months ago
Deep Review ⭐ 1,186
A collaboratively written review paper on deep learning, genomics, and precision medicine
most recent commit a year ago
Galaxy ⭐ 1,035
Data intensive science for everyone.
dependent packages 12total releases 13most recent commit 10 hours agopypi galaxy-util} Downloads
Pymatgen ⭐ 1,027
Python Materials Genomics (pymatgen) is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project.
dependent packages 135total releases 335most recent commit 2 days agopypi pymatgen} Downloads
Adam ⭐ 936
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
dependent packages 17total releases 14most recent commit 2 days ago
Vg ⭐ 868
tools for working with genome variation graphs
most recent commit a day ago
Hail ⭐ 846
Scalable genomic data analysis.
most recent commit a day ago
Getting Started With Genomics Tools And Resources ⭐ 800
Unix, R and python tools for genomics and data science
most recent commit 2 months ago
Applied Computational Genomics ⭐ 738
Applied Computational Genomics Course at UU: Spring 2020
most recent commit 8 months ago
Nucleus ⭐ 675
Python and C++ code for reading and writing genomics data.
dependent packages 2total releases 18most recent commit a year agopypi google-nucleus} Downloads
Seq ⭐ 610
A high-performance, Pythonic language for bioinformatics
most recent commit 4 months ago
Ncbi Genome Download ⭐ 576
Scripts to download genomes from the NCBI FTP servers
dependent packages 3total releases 23most recent commit a year agopypi ncbi-genome-download} Downloads
Bwa Mem2 ⭐ 572
The next version of bwa-mem
most recent commit a month ago
Goatools ⭐ 560
Python library to handle Gene Ontology (GO) terms
dependent packages 17total releases 42most recent commit 4 days agopypi goatools} Downloads
Jcvi ⭐ 548
Python library to facilitate genome assembly, annotation, and comparative genomics
total releases 79most recent commit 7 days ago
Deeptools ⭐ 538
Tools to process and analyze deep sequencing data.
most recent commit 6 days ago
Igv.js ⭐ 536
Embeddable genomic visualization component based on the Integrative Genomics Viewer
dependent packages 6total releases 86most recent commit 11 days agonpm igv} Downloads
Vcflib ⭐ 522
C++ library and cmdline tools for parsing and manipulating VCF files
most recent commit 7 days ago
Igv ⭐ 521
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
most recent commit 5 days ago
Biojava ⭐ 509
📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
dependent packages 13total releases 51most recent commit a month ago
Bowtie2 ⭐ 490
A fast and sensitive gapped read aligner
most recent commit a day ago
Cbioportal ⭐ 442
cBioPortal for Cancer Genomics
most recent commit 2 days ago
Orthofinder ⭐ 436
Phylogenetic orthology inference for comparative genomics
most recent commit 8 months ago
Megahit ⭐ 418
Ultra-fast and memory-efficient (meta-)genome assembler
most recent commit 2 months ago
Healthcare_ml ⭐ 407
A curated list of ML|NLP resources for healthcare.
most recent commit 4 months ago
Jbrowse ⭐ 401
A modern genome browser built with JavaScript and HTML5.
total releases 30most recent commit a year ago
Jvarkit ⭐ 390
Java utilities for Bioinformatics
most recent commit 5 days ago
Eggnog Mapper ⭐ 376
Fast genome-wide functional annotation through orthology assignment
most recent commit 5 months ago
Pyfaidx ⭐ 370
Efficient pythonic random access to fasta subsequences
most recent commit a month ago
Gggenomes ⭐ 355
A grammar of graphics for comparative genomics
most recent commit a month ago
Genomicspapers ⭐ 350
The Leek group guide to genomics papers
most recent commit 4 years ago
Maftools ⭐ 347
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
most recent commit 5 days ago
Scrna Seq_notes ⭐ 341
A list of scRNA-seq analysis tools
most recent commit 3 days ago
Postgui ⭐ 335
A React web application to query and share any PostgreSQL database.
most recent commit 10 months ago
Arvados ⭐ 332
An open source platform for managing and analyzing biomedical big data
total releases 6most recent commit 2 days ago
Delly ⭐ 320
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
most recent commit 6 days ago
Vcfanno ⭐ 314
annotate a VCF with other VCFs/BEDs/tabixed files
dependent packages 1total releases 40most recent commit 5 days ago
Cyvcf2 ⭐ 313
cython + htslib == fast VCF and BCF processing
dependent packages 37total releases 87most recent commit 19 days agopypi cyvcf2} Downloads
Hifiasm ⭐ 304
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
most recent commit 2 days ago
Minigraph ⭐ 301
Proof-of-concept seq-to-graph mapper and graph generator
most recent commit 14 days ago
Pyranges ⭐ 300
Performant Pythonic GenomicRanges
dependent packages 27total releases 107most recent commit 7 months agopypi pyranges} Downloads
Awesome Omics ⭐ 283
A collection of awesome things regarding all omics.
most recent commit 8 months ago
Hap.py ⭐ 283
Haplotype VCF comparison tools
most recent commit a year ago
Juicer ⭐ 279
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
most recent commit 5 months ago
Canvasxpress ⭐ 267
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
dependent packages 3total releases 33most recent commit 6 hours ago
Octopus ⭐ 262
Bayesian haplotype-based mutation calling
most recent commit 5 months ago
Bio.jl ⭐ 255
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
most recent commit 3 years ago
Genomeworks ⭐ 249
SDK for GPU accelerated genome assembly and analysis
most recent commit 5 months ago
Htsjdk ⭐ 247
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 82total releases 70most recent commit 5 days ago
Higlass ⭐ 247
Fast, flexible and extensible genome browser.
dependent packages 35total releases 232most recent commit 2 months agonpm higlass} Downloads
Dragonn ⭐ 245
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
most recent commit 5 months ago
Bedops ⭐ 244
🔬 BEDOPS: high-performance genomic feature operations
most recent commit 5 months ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 3 years ago
Genometools ⭐ 240
GenomeTools genome analysis system.
most recent commit 18 days ago
Sequenceserver ⭐ 238
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
total releases 65most recent commit 3 months ago
Comp Genomics Class ⭐ 236
Code and examples for JHU Computational Genomics class
most recent commit a year ago
Ideogram ⭐ 235
Chromosome visualization for the web
dependent packages 5total releases 68most recent commit 11 days agonpm ideogram} Downloads
Intermine ⭐ 228
A powerful open source data warehouse system
dependent packages 2total releases 7most recent commit 3 months ago
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83most recent commit 7 months ago
Ribbon ⭐ 219
A genome browser that shows long reads and complex variants better
most recent commit 3 months ago
Glow ⭐ 218
An open-source toolkit for large-scale genomic analysis
dependent packages 1total releases 8most recent commit 24 days ago
Flowcraft ⭐ 214
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
total releases 18most recent commit 3 years ago
Ga4gh Schemas ⭐ 213
Models and APIs for Genomic data. RETIRED 2018-01-24
total releases 12most recent commit a month ago
Sarek ⭐ 210
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
most recent commit 10 days ago
Kipoi ⭐ 210
Kipoi's model zoo API
dependent packages 6total releases 72most recent commit 4 months agopypi kipoi} Downloads
Janggu ⭐ 205
Deep learning infrastructure for genomics
total releases 19most recent commit a year ago
Deep Rules ⭐ 198
Ten Quick Tips for Deep Learning in Biology
most recent commit a year ago
Miniasm ⭐ 195
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
most recent commit 3 years ago
Rtg Tools ⭐ 194
RTG Tools: Utilities for accurate VCF comparison and manipulation
most recent commit 9 months ago
Vcfr ⭐ 193
Tools to work with variant call format files
dependent packages 12total releases 13most recent commit 2 months ago
Goleft ⭐ 192
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
dependent packages 1total releases 31most recent commit 2 months ago
Enformer Pytorch ⭐ 191
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
dependent packages 1total releases 73most recent commit 3 months agopypi enformer-pytorch} Downloads
Wgsim ⭐ 188
Reads simulator
most recent commit a year ago
Hgvs ⭐ 186
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 10total releases 101most recent commit 18 days agopypi hgvs} Downloads
Truvari ⭐ 186
Structural variant toolkit for VCFs
total releases 20most recent commit 3 days ago
Gwa_tutorial ⭐ 184
A comprehensive tutorial about GWAS and PRS
most recent commit 3 years ago
Aws Batch Genomics ⭐ 181
Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
most recent commit 3 years ago
Slivar ⭐ 178
genetic variant expressions, annotation, and filtering for great good.
most recent commit 15 days ago
Smoove ⭐ 173
structural variant calling and genotyping with existing tools, but, smoothly.
total releases 23most recent commit 7 months ago
Snp Sites ⭐ 173
Finds SNP sites from a multi-FASTA alignment file
most recent commit 2 years ago
Somalier ⭐ 172
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
most recent commit a month ago
Archive Datacarpentry ⭐ 167
Data Carpentry workshop materials
most recent commit 4 years ago
Awesome Bioinformatics Benchmarks ⭐ 167
A curated list of bioinformatics bench-marking papers and resources.
most recent commit a year ago
Artemis ⭐ 163
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
most recent commit 8 months ago
Miso Lims ⭐ 163
MISO: An open-source LIMS for NGS sequencing centres
most recent commit 2 days ago
Biomartr ⭐ 162
Genomic Data Retrieval with R
dependent packages 2total releases 16most recent commit 7 months ago
Gcp For Bioinformatics ⭐ 161
GCP for Bioinformatics Researchers
most recent commit a day ago
Dram ⭐ 154
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
total releases 21most recent commit 2 days ago
Genomics ⭐ 154
A collection of scripts and notes related to genomics and bioinformatics
most recent commit 3 months ago
Hicexplorer ⭐ 149
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
most recent commit 9 months ago
Msprime ⭐ 148
Simulate genealogical trees and genomic sequence data using population genetic models
dependent packages 2total releases 9most recent commit 18 days ago
Pathomicfusion ⭐ 148
Fusing Histology and Genomics via Deep Learning - IEEE TMI
most recent commit 3 months ago
Hts Nim ⭐ 148
nim wrapper for htslib for parsing genomics data files
most recent commit 2 months ago
Opencga ⭐ 148
An Open Computational Genomics Analysis platform for big data processing and analysis in genomics
total releases 24most recent commit 11 days ago
1-100 of 1,801 projects
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