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The Top 23 Genomics Open Source Projects

Open source projects categorized as Genomics
Categories > Science > Genomics
Biopython ⭐ 3,765
Official git repository for Biopython (originally converted from CVS)
dependent packages 1,262total releases 58most recent commit 5 days agopypi biopython} Downloads
Deepvariant ⭐ 2,869
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
Seurat ⭐ 1,938
R toolkit for single cell genomics
dependent packages 2total releases 16most recent commit 4 days ago
Deeplearning Biology ⭐ 1,846
A list of deep learning implementations in biology
most recent commit 5 months ago
Gatk ⭐ 1,496
Official code repository for GATK versions 4 and up
dependent packages 2total releases 46most recent commit 3 days ago
Minimap2 ⭐ 1,457
A versatile pairwise aligner for genomic and spliced nucleotide sequences
dependent packages 32total releases 27most recent commit 4 months agopypi mappy} Downloads
Bwa ⭐ 1,282
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
total releases 1most recent commit 5 months ago
Deep Review ⭐ 1,186
A collaboratively written review paper on deep learning, genomics, and precision medicine
most recent commit 2 years ago
Pymatgen ⭐ 1,166
Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.
dependent packages 197total releases 364most recent commit 2 days agopypi pymatgen} Downloads
Galaxy ⭐ 1,158
Data intensive science for everyone.
dependent packages 22total releases 25most recent commit 6 hours agopypi galaxy-util} Downloads
Vg ⭐ 963
tools for working with genome variation graphs
most recent commit 3 days ago
Getting Started With Genomics Tools And Resources ⭐ 957
Unix, R and python tools for genomics and data science
most recent commit 13 hours ago
Adam ⭐ 955
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 a month ago
Hail ⭐ 889
Cloud-native genomic dataframes and batch computing
dependent packages 16total releases 144most recent commit 3 days agopypi hail} Downloads
Ncbi Genome Download ⭐ 784
Scripts to download genomes from the NCBI FTP servers
dependent packages 3total releases 23most recent commit 2 months agopypi ncbi-genome-download} Downloads
Applied Computational Genomics ⭐ 738
Applied Computational Genomics Course at UU: Spring 2020
most recent commit a year ago
Nucleus ⭐ 675
Python and C++ code for reading and writing genomics data.
dependent packages 2total releases 18most recent commit 2 years agopypi google-nucleus} Downloads
Goatools ⭐ 644
Python library to handle Gene Ontology (GO) terms
dependent packages 17total releases 42most recent commit 4 days agopypi goatools} Downloads
Seq ⭐ 624
A high-performance, Pythonic language for bioinformatics
most recent commit 10 months ago
Bwa Mem2 ⭐ 620
The next version of bwa-mem
most recent commit 2 months ago
Jcvi ⭐ 616
Python library to facilitate genome assembly, annotation, and comparative genomics
total releases 79most recent commit 4 days ago
Deeptools ⭐ 601
Tools to process and analyze deep sequencing data.
most recent commit 5 days ago
Igv.js ⭐ 591
Embeddable genomic visualization component based on the Integrative Genomics Viewer
dependent packages 6total releases 86most recent commit 10 hours agonpm igv} Downloads
The 10 Most Depended On Genomics Open Source Projects
Biopython ⭐ 3,765
Official git repository for Biopython (originally converted from CVS)
dependent packages 1,262total releases 58latest release February 13, 2023most recent commit 5 days agopypi biopython} Downloads
Htsjdk ⭐ 265
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 82total releases 74latest release November 23, 2022most recent commit a month ago
Cyvcf2 ⭐ 332
cython + htslib == fast VCF and BCF processing
dependent packages 37total releases 87latest release March 15, 2022most recent commit 11 days agopypi cyvcf2} Downloads
Higlass ⭐ 277
Fast, flexible and extensible genome browser.
dependent packages 35total releases 232latest release April 25, 2022most recent commit 12 days agonpm higlass} Downloads
Minimap2 ⭐ 1,457
A versatile pairwise aligner for genomic and spliced nucleotide sequences
dependent packages 32total releases 27latest release December 26, 2021most recent commit 4 months agopypi mappy} Downloads
Galaxy ⭐ 1,158
Data intensive science for everyone.
dependent packages 22total releases 25latest release July 30, 2023most recent commit 6 hours agopypi galaxy-util} Downloads
Goatools ⭐ 644
Python library to handle Gene Ontology (GO) terms
dependent packages 17total releases 42latest release March 07, 2022most recent commit 4 days agopypi goatools} Downloads
Hail ⭐ 889
Cloud-native genomic dataframes and batch computing
dependent packages 16total releases 144latest release September 21, 2023most recent commit 3 days agopypi hail} Downloads
The 10 Latest Releases In Genomics Open Source Projects
Hail ⭐ 889
Cloud-native genomic dataframes and batch computing
dependent packages 16total releases 144latest release September 21, 2023most recent commit 3 days agopypi hail} Downloads
Galaxy ⭐ 1,158
Data intensive science for everyone.
dependent packages 22total releases 25latest release July 30, 2023most recent commit 6 hours agopypi galaxy-util} Downloads
Gatk ⭐ 1,496
Official code repository for GATK versions 4 and up
dependent packages 2total releases 46latest release March 16, 2023most recent commit 3 days ago
Biopython ⭐ 3,765
Official git repository for Biopython (originally converted from CVS)
dependent packages 1,262total releases 58latest release February 13, 2023most recent commit 5 days agopypi biopython} Downloads
Ideogram ⭐ 258
Chromosome visualization for the web
dependent packages 6total releases 71latest release December 07, 2022most recent commit a month agonpm ideogram} Downloads
Canvasxpress ⭐ 281
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
dependent packages 3total releases 38latest release December 01, 2022most recent commit 4 days ago
Htsjdk ⭐ 265
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 82total releases 74latest release November 23, 2022most recent commit a month ago
Hgvs ⭐ 218
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 11total releases 104latest release November 21, 2022most recent commit 14 days agopypi hgvs} Downloads
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