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The Top 23 Python Bioinformatics Genomics Open Source Projects

Open source projects categorized as Python Bioinformatics Genomics
Categories > Data Processing > Bioinformatics
Categories > Science > Genomics
Biopython ⭐ 3,918
Official git repository for Biopython (originally converted from CVS)
dependent packages 1,373total releases 58most recent commit 3 months agopypi biopython} Downloads
Deepvariant ⭐ 2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
most recent commit 5 months ago
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30most recent commit 3 months agopypi galaxy-util} Downloads
Adam ⭐ 966
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 3 months ago
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146most recent commit 3 months agopypi hail} Downloads
Ncbi Genome Download ⭐ 784
Scripts to download genomes from the NCBI FTP servers
dependent packages 6total releases 25most recent commit 9 months agopypi ncbi-genome-download} Downloads
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97most recent commit 4 months agopypi jcvi} Downloads
Deeptools ⭐ 644
Tools to process and analyze deep sequencing data.
most recent commit 18 days ago
Seq ⭐ 624
A high-performance, Pythonic language for bioinformatics
most recent commit a year ago
Pycirclize ⭐ 476
Circular visualization in Python (Circos Plot, Chord Diagram)
dependent packages 3total releases 13most recent commit 4 months agopypi pycirclize} Downloads
Pyfaidx ⭐ 427
Efficient pythonic random access to fasta subsequences
dependent packages 119total releases 86most recent commit 3 months agopypi pyfaidx} Downloads
Arvados ⭐ 354
An open source platform for managing and analyzing biomedical big data
total releases 9most recent commit 3 months ago
Canvasxpress ⭐ 282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
dependent packages 4total releases 43most recent commit 3 months ago
Genometools ⭐ 261
GenomeTools genome analysis system.
most recent commit 6 months ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Intermine ⭐ 228
A powerful open source data warehouse system
dependent packages 2total releases 8most recent commit 2 years ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104most recent commit 3 months agopypi hgvs} Downloads
Hicexplorer ⭐ 197
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
most recent commit 5 months ago
Circlator ⭐ 193
A tool to circularize genome assemblies
total releases 33most recent commit 8 months ago
Cooler ⭐ 183
A cool place to store your Hi-C
dependent packages 27total releases 45most recent commit 3 months agopypi cooler} Downloads
Pygenomeviz ⭐ 177
A genome visualization python package for comparative genomics
dependent packages 1total releases 23most recent commit 6 months agopypi pygenomeviz} Downloads
Readfish ⭐ 152
CLI tool for flexible and fast adaptive sampling on ONT sequencers
total releases 9most recent commit 4 months ago
Gatk Sv ⭐ 148
A structural variation pipeline for short-read sequencing
most recent commit 3 months ago
The 10 Most Depended On Python Bioinformatics Genomics Open Source Projects
Biopython ⭐ 3,918
Official git repository for Biopython (originally converted from CVS)
dependent packages 1,373total releases 58latest release February 13, 2023most recent commit 3 months agopypi biopython} Downloads
Pyfaidx ⭐ 427
Efficient pythonic random access to fasta subsequences
dependent packages 119total releases 86latest release September 22, 2023most recent commit 3 months agopypi pyfaidx} Downloads
Cooler ⭐ 183
A cool place to store your Hi-C
dependent packages 27total releases 45latest release September 11, 2023most recent commit 3 months agopypi cooler} Downloads
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36latest release October 10, 2023most recent commit 3 months agopypi tskit} Downloads
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months agopypi hgvs} Downloads
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62latest release July 10, 2023most recent commit 3 months agopypi bioutils} Downloads
The 10 Latest Releases In Python Bioinformatics Genomics Open Source Projects
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
Algebra ⭐ 10
A Boolean Algebra for Genetic Variants
dependent packages 2total releases 18latest release December 04, 2023most recent commit 3 months agopypi mutalyzer-algebra} Downloads
Gecco ⭐ 45
GEne Cluster prediction with COnditional random fields.
total releases 29latest release November 23, 2023most recent commit 5 months ago
Glue Genes ⭐ 7
glue for genomics and transcriptomics
total releases 7latest release November 22, 2023most recent commit 5 months ago
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Biokit ⭐ 20
a versatile toolkit for processing and analyzing diverse types of sequence data
total releases 13latest release November 11, 2023most recent commit 4 months ago
Vrs Python ⭐ 44
GA4GH Variation Representation Python Implementation
dependent packages 7total releases 48latest release November 09, 2023most recent commit 3 months agopypi ga4gh.vrs} Downloads
Canvasxpress ⭐ 282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
dependent packages 4total releases 43latest release November 08, 2023most recent commit 3 months ago
Aniclustermap ⭐ 38
A tool for drawing ANI clustermap between all-vs-all microbial genomes
total releases 5latest release November 07, 2023most recent commit 6 months ago
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