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    62 repositories

    • onecodex

      Public
      Command line interface and Python client library for the One Codex API
      Python
      •
      MIT License
      •12•25•29•4•Updated Mar 16, 2026Mar 16, 2026

    • taxonomy

      Public
      Python and Rust library for loading, saving, and manipulating taxonomic trees
      Rust
      •
      MIT License
      •3•53•8•0•Updated Mar 15, 2026Mar 15, 2026

    • taxonomy-time-machine

      Public
      NCBI Taxonomy History Browser
      Vue
      •
      MIT License
      •1•10•2•1•Updated Feb 15, 2026Feb 15, 2026

    • needletail

      Public
      Fast FASTX parsing and k-mer methods in Rust
      Rust
      •
      MIT License
      •29•210•14•0•Updated Jan 27, 2026Jan 27, 2026

    • docker-onecodex-notebook

      Public
      Docker image with a Jupyter notebook environment for embedded use on One Codex
      HTML
      •
      MIT License
      •1•2•3•3•Updated Jan 21, 2026Jan 21, 2026

    • docker-onecodex-cli

      Public
      DEPRECATED: Old image with One Codex CLI - please install directly now
      Python
      •0•0•0•1•Updated Dec 8, 2025Dec 8, 2025

    • gdl

      Public
      A fast, easy-to-use, command-line tool for downloading genome assemblies from NCBI GenBank (RefSeq).
      Rust
      •
      MIT License
      •1•1•0•0•Updated Jul 22, 2025Jul 22, 2025

    • potion

      Public
      Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine
      Python
      •
      Other
      •50•0•0•1•Updated Jul 14, 2025Jul 14, 2025

    • rust-bfield

      Public
      B-field implementation in Rust
      Rust
      •
      Apache License 2.0
      •4•205•4•0•Updated Jun 24, 2025Jun 24, 2025

    • finch-rs

      Public
      A genomic minhashing implementation in Rust
      Rust
      •
      MIT License
      •8•103•13•2•Updated Jun 17, 2025Jun 17, 2025

    • basespace-python-sdk

      Public
      BaseSpace Python SDK
      Python
      •
      Apache License 2.0
      •30•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • chrononaut

      Public
      A history mixin with audit logging, record locking, and time travel for FlaskSQLAlchemy
      pythonflaskpostgres
      pythonflaskpostgressqlalchemyflask-sqlalchemy
      Python
      •
      MIT License
      •4•19•3•2•Updated Mar 5, 2025Mar 5, 2025

    • mmap-bitvec

      Public
      Rust implementation of a mmap-based bit vector
      Rust
      •
      MIT License
      •0•6•4•0•Updated Oct 6, 2023Oct 6, 2023

    • sars-cov-2

      Public
      SARS-CoV-2 variant calling and consensus assembly pipeline
      Jupyter Notebook
      •
      MIT License
      •6•26•1•1•Updated Sep 18, 2023Sep 18, 2023

    • flask-login

      Public
      Flask user session management.
      Python
      •
      MIT License
      •817•0•0•0•Updated Jul 31, 2023Jul 31, 2023

    • altair_saver

      Public
      Altair extension for saving charts in a variety of formats.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •32•0•0•0•Updated Jul 19, 2023Jul 19, 2023

    • flask-limiter

      Public
      rate limiting extension for flask applications
      Python
      •
      MIT License
      •128•0•0•0•Updated Mar 29, 2023Mar 29, 2023

    • genome_portal_api

      Public
      Python package to access and download data from the ATCC Genome Portal (https://genomes.atcc.org/)
      Python
      •
      Other
      •5•0•0•0•Updated Mar 10, 2023Mar 10, 2023

    • flask-smorest

      Public
      DB agnostic framework to build auto-documented REST APIs with Flask and marshmallow
      Python
      •
      MIT License
      •76•0•0•1•Updated Feb 9, 2023Feb 9, 2023

    • assembly-annotation-tools

      Public
      Dockerfile
      •
      MIT License
      •1•1•0•4•Updated Dec 8, 2022Dec 8, 2022

    • limit-secrets-test

      Public
      This repository's sole purpose is to verify that secrets may indeed be limited to a selected branch
      0•0•0•0•Updated Jun 14, 2022Jun 14, 2022

    • sdust

      Public
      Rust
      •
      MIT License
      •0•0•0•0•Updated May 5, 2022May 5, 2022

    • template-python

      Public template
      Template Python repository
      Makefile
      •
      MIT License
      •0•0•0•3•Updated Nov 15, 2021Nov 15, 2021

    • laptop

      Public archive
      A shell script to set up a macOS laptop for web and mobile development.
      Shell
      •
      MIT License
      •1.9k•0•0•0•Updated Aug 19, 2021Aug 19, 2021

    • abricate

      Public
      :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
      Perl
      •
      GNU General Public License v2.0
      •102•0•0•0•Updated Jul 2, 2021Jul 2, 2021

    • terraform-aws-eks

      Public
      Terraform module to create an Elastic Kubernetes (EKS) cluster and associated worker instances on AWS
      HCL
      •
      Other
      •4.4k•0•0•0•Updated May 25, 2021May 25, 2021

    • metagraph

      Public
      Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
      C++
      •
      GNU General Public License v3.0
      •26•0•0•0•Updated Apr 14, 2021Apr 14, 2021

    • docker-shovill

      Public
      Docker container for tseemann/shovill
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2021Jan 31, 2021

    • docker-unicycler

      Public
      Docker container for the Unicycler hybrid assembler
      Dockerfile
      •
      MIT License
      •1•2•0•1•Updated Jan 31, 2021Jan 31, 2021

    • public-dockerfiles

      Public
      Public Dockerfiles
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2021Jan 31, 2021