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    41 repositories

    • cnpy

      Public
      library to read/write .npy and .npz files in C/C++
      C++
      •
      MIT License
      •326•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • hmmer-benchmarking

      Public
      Hmmsearch Benchmarking Study
      Jupyter Notebook
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • zstr

      Public
      A C++ header-only ZLib wrapper
      C++
      •
      MIT License
      •77•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • jgi-scalable-toolkit-workshop-24

      Public
      2024 JGI's Scalable Metagenomics Toolbox Workshop
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 16, 2024Oct 16, 2024

    • axolotl

      Public
      Axolotl is a Python library for scalable genome analysis, addressing the gap in tools for handling the rapid growth of genomic data with easy parallel processing.
      pythonscalablegenomicsdistributed-computingaxolotlmetagenome
      Python
      •
      Other
      •1•6•2•0•Updated Sep 30, 2024Sep 30, 2024

    • cromwell

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •375•0•0•0•Updated May 11, 2023May 11, 2023

    • jgi-globus-timer

      Public
      Python
      •0•1•2•0•Updated Sep 1, 2022Sep 1, 2022

    • alphafold

      Public
      Open source code for AlphaFold.
      Python
      •
      Apache License 2.0
      •2.5k•0•0•0•Updated Oct 25, 2021Oct 25, 2021

    • HybridLPA

      Public
      MPI version of Sparc
      C++
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Dec 17, 2020Dec 17, 2020

    • behave-command-line

      Public
      Feature testing for command line tools
      Python
      •
      Other
      •1•0•4•0•Updated Oct 26, 2019Oct 26, 2019

    • minimap2

      Public
      A fast pairwise aligner for genomic and spliced nucleotide sequences
      C
      •
      Other
      •445•0•0•0•Updated Jul 3, 2019Jul 3, 2019

    • yacrd_analysis

      Public
      Python
      •0•0•0•0•Updated May 15, 2019May 15, 2019

    • minimap

      Public
      Experimental tool to find approximate mapping positions between long sequences
      C
      •
      MIT License
      •29•1•0•0•Updated Apr 20, 2018Apr 20, 2018

    • albacore

      Public
      Dockerfile for the Albacore basecaller from Oxford Nanopore
      GNU General Public License v3.0
      •4•3•0•0•Updated Mar 8, 2018Mar 8, 2018

    • poretools

      Public
      a toolkit for working with Oxford nanopore data
      Jupyter Notebook
      •
      MIT License
      •86•0•0•0•Updated Mar 5, 2018Mar 5, 2018

    • auto-qc

      Public
      Python
      •
      Other
      •1•1•0•0•Updated Feb 22, 2018Feb 22, 2018

    • JGI-Data-Science

      Public
      repository for notebooks used in the JGI data science training series
      Jupyter Notebook
      •1•0•0•0•Updated Feb 14, 2018Feb 14, 2018

    • biopig

      Public archive
      Java
      •
      Other
      •7•9•1•0•Updated Nov 2, 2017Nov 2, 2017

    • jumbomem

      Public
      C
      •
      Other
      •0•0•0•0•Updated Sep 21, 2017Sep 21, 2017

    • docker.openmpi

      Public
      A scalable OpenMPI runtime container for Docker
      Python
      •66•0•0•0•Updated May 13, 2017May 13, 2017

    • racon

      Public
      Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116
      C++
      •
      MIT License
      •51•0•0•0•Updated May 11, 2017May 11, 2017

    • nanosv

      Public
      SV caller for nanopore data
      Perl
      •
      MIT License
      •22•0•0•0•Updated May 8, 2017May 8, 2017

    • graphmap

      Public
      GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html
      C++
      •
      MIT License
      •44•0•0•0•Updated Apr 21, 2017Apr 21, 2017

    • canu

      Public
      A single molecule sequence assembler for genomes large and small.
      C++
      •179•0•0•0•Updated Apr 20, 2017Apr 20, 2017

    • seqlib

      Public
      A codebase for sequence analysis projects. Highly experimental and in development.
      HTML
      •
      MIT License
      •4•0•0•0•Updated Mar 29, 2017Mar 29, 2017

    • berkeley_upc-docker

      Public
      A container for Berkeley UPC.
      MIT License
      •0•0•0•0•Updated Mar 25, 2017Mar 25, 2017

    • nanonet

      Public
      First generation RNN basecaller
      C++
      •
      Mozilla Public License 2.0
      •19•0•0•0•Updated Nov 21, 2016Nov 21, 2016

    • pigz

      Public
      A parallel implementation of gzip for modern multi-processor, multi-core machines.
      C
      •185•0•0•0•Updated Jun 10, 2016Jun 10, 2016

    • minoTour

      Public
      Real time data analysis tools for the minION sequencing platform.
      PHP
      •
      GNU General Public License v3.0
      •13•0•0•0•Updated May 19, 2016May 19, 2016

    • currennt

      Public
      Modified fork of CURRENNT https://sourceforge.net/projects/currennt/
      C++
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Mar 14, 2016Mar 14, 2016