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The Top 23 Java Genomics Open Source Projects

Open source projects categorized as Java Genomics

Categories > Science > Genomics

Categories > Programming Languages > Java

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

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

most recent commit 3 months ago

Biojava ⭐ 564

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

dependent packages 16total releases 56most recent commit 3 months ago

Cbioportal ⭐ 535

cBioPortal for Cancer Genomics

most recent commit 3 months ago

Jvarkit ⭐ 440

Java utilities for Bioinformatics

most recent commit 5 months ago

A Java API for high-throughput sequencing data (HTS) formats.

dependent packages 87total releases 78most recent commit 4 months ago

Rtg Tools ⭐ 260

RTG Tools: Utilities for accurate VCF comparison and manipulation

most recent commit 3 months ago

Intermine ⭐ 228

A powerful open source data warehouse system

dependent packages 2total releases 8most recent commit 2 years ago

Miso Lims ⭐ 214

MISO: An open-source LIMS for NGS sequencing centres

most recent commit 3 months ago

Artemis ⭐ 191

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 a year ago

Exomiser ⭐ 174

A Tool to Annotate and Prioritize Exome Variants

most recent commit 3 months ago

Opencga ⭐ 164

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is not maintained and develop by its parent company Zetta Genomics. Please contact [email protected] for bug report and feature requests.

dependent packages 8total releases 57most recent commit 3 months ago

Hmftools ⭐ 163

Various algorithms for analysing genomics data

most recent commit 3 months ago

Cloud Pipeline ⭐ 137

Cloud agnostic genomics analysis, scientific computation and storage platform

most recent commit 3 months ago

Dnanalyzer ⭐ 122

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

most recent commit 5 months ago

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

most recent commit 3 months ago

Dockerflow ⭐ 90

Dockerflow is a workflow runner that uses Dataflow to run a series of tasks in Docker with the Pipelines API

most recent commit 6 years ago

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

dependent packages 2total releases 35most recent commit 3 months ago

most recent commit 2 years ago

Liblevenshtein Java ⭐ 40

Various utilities regarding Levenshtein transducers. (Java)

dependent packages 10total releases 4most recent commit 6 years ago

Genome Nexus ⭐ 38

Backend server for Genome Nexus

most recent commit 4 months ago

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

most recent commit 4 months ago

Dataflow Java ⭐ 35

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

dependent packages 1total releases 26most recent commit 5 years ago

The 10 Most Depended On Java Genomics Open Source Projects

A Java API for high-throughput sequencing data (HTS) formats.

dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago

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 14latest release December 16, 2020most recent commit 3 months ago

Biojava ⭐ 564

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

dependent packages 16total releases 56latest release June 02, 2023most recent commit 3 months ago

Liblevenshtein Java ⭐ 40

Various utilities regarding Levenshtein transducers. (Java)

dependent packages 10total releases 4latest release May 29, 2016most recent commit 6 years ago

Opencga ⭐ 164

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is not maintained and develop by its parent company Zetta Genomics. Please contact [email protected] for bug report and feature requests.

dependent packages 8total releases 57latest release November 20, 2023most recent commit 3 months ago

A library for manipulating bioinformatics sequencing formats in Apache Spark

dependent packages 3total releases 10latest release February 09, 2021most recent commit 8 months ago

phenol: Phenotype ontology library

dependent packages 3total releases 16latest release May 12, 2022most recent commit 4 months ago

Intermine ⭐ 228

A powerful open source data warehouse system

dependent packages 2total releases 8latest release August 26, 2022most recent commit 2 years ago

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

dependent packages 2total releases 35latest release October 12, 2023most recent commit 3 months ago

Dataflow Java ⭐ 35

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

dependent packages 1total releases 26latest release October 23, 2017most recent commit 5 years ago

The 10 Latest Releases In Java Genomics Open Source Projects

Opencga ⭐ 164

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is not maintained and develop by its parent company Zetta Genomics. Please contact [email protected] for bug report and feature requests.

dependent packages 8total releases 57latest release November 20, 2023most recent commit 3 months ago

A Java API for high-throughput sequencing data (HTS) formats.

dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago

Genomicsdb ⭐ 88

High performance data storage for importing, querying and transforming variants.

dependent packages 2total releases 35latest release October 12, 2023most recent commit 3 months ago

Biojava ⭐ 564

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

dependent packages 16total releases 56latest release June 02, 2023most recent commit 3 months ago

Intermine ⭐ 228

A powerful open source data warehouse system

dependent packages 2total releases 8latest release August 26, 2022most recent commit 2 years ago

phenol: Phenotype ontology library

dependent packages 3total releases 16latest release May 12, 2022most recent commit 4 months ago

A library for manipulating bioinformatics sequencing formats in Apache Spark

dependent packages 3total releases 10latest release February 09, 2021most recent commit 8 months ago

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 14latest release December 16, 2020most recent commit 3 months ago

Python Library for data analysis based on GMQL

total releases 16latest release June 19, 2019most recent commit 2 years ago

Dataflow Java ⭐ 35

Google Cloud Dataflow pipelines such as Identity-By-State as well as useful utility classes.

dependent packages 1total releases 26latest release October 23, 2017most recent commit 5 years ago

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