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    64 repositories

    • fgbio

      Public
      Tools for working with genomic and high throughput sequencing data.
      bioinformaticsscalagenomicsngsumianalyzing-genomic-datafgbiomolecular-indexes
      Scala
      •
      MIT License
      •75•348•45•26•Updated Oct 24, 2025Oct 24, 2025

    • commons

      Public
      Common scala utilities
      Scala
      •
      MIT License
      •3•5•10•1•Updated Oct 24, 2025Oct 24, 2025

    • sopt

      Public
      An argument parsing library for Scala
      scalaargument-parsing
      Scala
      •
      MIT License
      •0•11•4•2•Updated Oct 24, 2025Oct 24, 2025

    • fglatch

      Public
      CLI and Python extensions for the LatchBio platform.
      Python
      •
      MIT License
      •0•0•8•0•Updated Oct 21, 2025Oct 21, 2025

    • fqtk

      Public
      Fast FASTQ sample demultiplexing in Rust.
      rustbioinformaticsgenomics
      Rust
      •
      MIT License
      •3•66•6•3•Updated Oct 19, 2025Oct 19, 2025

    • fgpyo

      Public
      Quality of life improvements for Bioinformatics in Python.
      pythonbioinformaticsgenomics
      Python
      •
      Other
      •3•31•26•8•Updated Oct 2, 2025Oct 2, 2025

    • pybedlite

      Public
      Lightweight Python interfaces for reading, writing, and querying genomic regions (BED)
      pythonbioinformaticsgenomicsbed-files
      Python
      •
      Other
      •1•14•1•0•Updated Sep 30, 2025Sep 30, 2025

    • fetch-through-merge-base

      Public
      A GitHub Action for fetching PR commits through the merge-base
      Python
      •
      MIT License
      •0•0•1•1•Updated Sep 29, 2025Sep 29, 2025

    • prymer

      Public
      Python Primer Design Library
      bioinformaticsgenomicsprimer-design
      Python
      •
      MIT License
      •0•14•35•1•Updated Sep 29, 2025Sep 29, 2025

    • pybwa

      Public
      Python language bindings for bwa
      bioinformaticsgenomics
      Cython
      •
      MIT License
      •0•11•3•1•Updated Sep 24, 2025Sep 24, 2025

    • nf-dotenv

      Public
      Automatically source dotenv files into your Nextflow scope
      dotenvnextflow
      Groovy
      •
      Other
      •0•9•2•1•Updated Sep 24, 2025Sep 24, 2025

    • viral-pipelines

      Public
      viral-ngs: complete pipelines
      WDL
      •
      Other
      •29•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • warp

      Public
      WDL Analysis Research Pipelines
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •111•1•0•1•Updated Sep 15, 2025Sep 15, 2025

    • nf-core-modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •912•0•0•1•Updated Sep 14, 2025Sep 14, 2025

    • gatk

      Public
      Official code repository for GATK versions 4 and up
      Java
      •
      Other
      •617•0•0•0•Updated Sep 3, 2025Sep 3, 2025

    • .github

      Public
      MIT License
      •0•2•0•0•Updated Aug 6, 2025Aug 6, 2025

    • dxCompiler

      Public
      WDL and CWL compiler for the DNAnexus platform
      Scala
      •
      Apache License 2.0
      •18•0•0•0•Updated Jun 16, 2025Jun 16, 2025

    • setup-latch

      Public
      TypeScript
      •
      MIT License
      •3•6•7•0•Updated Jun 6, 2025Jun 6, 2025

    • fgsmk

      Public
      Supporting Python functions for running Snakemake workflows
      Python
      •
      MIT License
      •0•0•5•0•Updated Jun 4, 2025Jun 4, 2025

    • bwa-aln-interactive

      Public
      BWA aln interactive: Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
      C
      •
      GNU General Public License v3.0
      •0•0•4•0•Updated Jun 2, 2025Jun 2, 2025

    • fgoxide

      Public
      Quality of life improvements in Rust.
      Rust
      •
      MIT License
      •4•5•2•1•Updated May 23, 2025May 23, 2025

    • nf-fgbio

      Public
      Use various fgbio functions and classes in your Nextflow scope.
      Groovy
      •
      Other
      •0•5•1•0•Updated May 21, 2025May 21, 2025

    • code-medium

      Public
      Browser extension that simplifies writing code in Medium posts. Quickly create and edit Github Gists without leaving the editor
      JavaScript
      •
      Mozilla Public License 2.0
      •7•0•0•0•Updated May 19, 2025May 19, 2025

    • gha-timer

      Public
      Time and group logs for GitHub actions
      Python
      •
      MIT License
      •0•2•0•0•Updated Apr 30, 2025Apr 30, 2025

    • stitch

      Public
      Stitch is a toolkit for analysis of chimeric reads in sequencing data
      Rust
      •
      MIT License
      •4•10•14•0•Updated Apr 29, 2025Apr 29, 2025

    • uv-docker-example

      Public
      An example of using uv in Docker images
      Dockerfile
      •56•0•0•0•Updated Apr 28, 2025Apr 28, 2025

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •441•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • betabinom

      Public
      Maintained fork of `countdata`
      C
      •
      Other
      •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • bgzf

      Public
      Rust
      •0•2•0•0•Updated Apr 11, 2025Apr 11, 2025

    • pyfgaws

      Public
      Python tools and APIs for working with AWS
      pythonawsbioinformaticsaws-batchaws-logs
      Python
      •
      MIT License
      •0•9•7•1•Updated Apr 11, 2025Apr 11, 2025