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@bigdatagenomics Big Data Genomics

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    23 repositories

    • adam

      Public
      ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
      pythonjavabioinformaticsrscalabig-datasparkavrogenomicsparquet
      Scala
      •
      Apache License 2.0
      •316•1k•35•5•Updated Jul 12, 2025Jul 12, 2025

    • convert

      Public
      Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.
      Java
      •
      Apache License 2.0
      •5•0•2•1•Updated Jul 12, 2025Jul 12, 2025

    • utils

      Public
      General utility code used across BDG products. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •26•18•2•1•Updated May 6, 2025May 6, 2025

    • cannoli

      Public
      Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •17•41•1•0•Updated Mar 2, 2025Mar 2, 2025

    • bdg-formats

      Public
      Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
      Shell
      •
      Apache License 2.0
      •36•41•1•1•Updated Feb 12, 2025Feb 12, 2025

    • bigdatagenomics.github.io

      Public
      Web Site for the Big Data Genomics Group
      HTML
      •7•10•0•0•Updated Sep 3, 2023Sep 3, 2023

    • mango

      Public
      A scalable genome browser. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •31•126•57•7•Updated Dec 2, 2022Dec 2, 2022

    • workflows

      Public
      Toil workflows for bigdatagenomics tools. Apache 2 licensed.
      Python
      •
      Apache License 2.0
      •5•5•8•1•Updated Apr 22, 2021Apr 22, 2021

    • jenkins-docker

      Public
      Dockerfile
      •
      Apache License 2.0
      •2•1•0•1•Updated Aug 23, 2020Aug 23, 2020

    • deca

      Public
      Distributed exome CNV analyzer. Apache 2 licensed.
      Scala
      •
      Other
      •4•3•9•1•Updated Oct 15, 2019Oct 15, 2019

    • awesome-adam

      Public
      Awesome list of applications that extend Big Data Genomics ADAM. CC0 licensed.
      4•11•0•0•Updated Jul 11, 2019Jul 11, 2019

    • avocado

      Public
      A Variant Caller, Distributed. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •41•71•19•6•Updated Mar 11, 2019Mar 11, 2019

    • gnocchi

      Public
      Scala
      •
      Apache License 2.0
      •10•6•10•1•Updated Apr 24, 2018Apr 24, 2018

    • lime

      Public
      Distributed Set Theory for Genomics
      Scala
      •
      Other
      •3•5•7•2•Updated Mar 27, 2018Mar 27, 2018

    • rice

      Public
      An RNA pipeline built on top of ADAM. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •17•19•7•2•Updated Jan 19, 2018Jan 19, 2018

    • quinine

      Public
      A refreshing treatment for all quality control ailments. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •6•2•5•2•Updated Oct 13, 2016Oct 13, 2016

    • toil-wdl-api

      Public
      Exemplar API that mediates Toil with a WDL front-end and workflow tracking.
      Java
      •
      Apache License 2.0
      •1•1•0•1•Updated Aug 1, 2016Aug 1, 2016

    • eggo

      Public
      Ready-to-go Parquet-formatted public 'omics datasets
      Python
      •
      Apache License 2.0
      •8•30•21•3•Updated Nov 2, 2015Nov 2, 2015

    • recipes

      Public
      Recipes using BDG projects. Apache 2 licensed.
      Shell
      •
      Apache License 2.0
      •3•4•1•0•Updated Mar 25, 2015Mar 25, 2015

    • PacMin

      Public
      Assembler for PacBio reads. Apache 2 licensed.
      Scala
      •
      Apache License 2.0
      •3•3•4•0•Updated Mar 14, 2015Mar 14, 2015

    • corretto

      Public
      Read error correction utilities.
      Apache License 2.0
      •2•0•2•0•Updated Mar 1, 2015Mar 1, 2015

    • mango-notebook

      Public
      Notebook tools for Big Data Genomics. Apache 2 licensed.
      JavaScript
      •
      Apache License 2.0
      •653•3•0•0•Updated Mar 1, 2015Mar 1, 2015

    • bdg-services

      Public
      Utility classes for wrapping services or other interfaces around a Spark/ADAM cluster. Apache 2 licensed.
      Java
      •
      Apache License 2.0
      •8•5•2•0•Updated Nov 17, 2014Nov 17, 2014