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    • onecodex

      Public
      Command line interface and Python client library for the One Codex API
      Python
      MIT License
      1225294Updated Mar 16, 2026Mar 16, 2026
    • taxonomy

      Public
      Python and Rust library for loading, saving, and manipulating taxonomic trees
      Rust
      MIT License
      35380Updated Mar 15, 2026Mar 15, 2026
    • NCBI Taxonomy History Browser
      Vue
      MIT License
      11021Updated Feb 15, 2026Feb 15, 2026
    • Fast FASTX parsing and k-mer methods in Rust
      Rust
      MIT License
      29210140Updated Jan 27, 2026Jan 27, 2026
    • Docker image with a Jupyter notebook environment for embedded use on One Codex
      HTML
      MIT License
      1233Updated Jan 21, 2026Jan 21, 2026
    • DEPRECATED: Old image with One Codex CLI - please install directly now
      Python
      0001Updated 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
      1100Updated Jul 22, 2025Jul 22, 2025
    • potion

      Public
      Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine
      Python
      Other
      50001Updated Jul 14, 2025Jul 14, 2025
    • B-field implementation in Rust
      Rust
      Apache License 2.0
      420540Updated Jun 24, 2025Jun 24, 2025
    • finch-rs

      Public
      A genomic minhashing implementation in Rust
      Rust
      MIT License
      8103132Updated Jun 17, 2025Jun 17, 2025
    • BaseSpace Python SDK
      Python
      Apache License 2.0
      30000Updated Mar 24, 2025Mar 24, 2025
    • A history mixin with audit logging, record locking, and time travel for FlaskSQLAlchemy
      Python
      MIT License
      41932Updated Mar 5, 2025Mar 5, 2025
    • Rust implementation of a mmap-based bit vector
      Rust
      MIT License
      0640Updated Oct 6, 2023Oct 6, 2023
    • SARS-CoV-2 variant calling and consensus assembly pipeline
      Jupyter Notebook
      MIT License
      62611Updated Sep 18, 2023Sep 18, 2023
    • Flask user session management.
      Python
      MIT License
      817000Updated Jul 31, 2023Jul 31, 2023
    • Altair extension for saving charts in a variety of formats.
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      32000Updated Jul 19, 2023Jul 19, 2023
    • rate limiting extension for flask applications
      Python
      MIT License
      128000Updated Mar 29, 2023Mar 29, 2023
    • Python package to access and download data from the ATCC Genome Portal (https://genomes.atcc.org/)
      Python
      Other
      5000Updated Mar 10, 2023Mar 10, 2023
    • DB agnostic framework to build auto-documented REST APIs with Flask and marshmallow
      Python
      MIT License
      76001Updated Feb 9, 2023Feb 9, 2023
    • Dockerfile
      MIT License
      1104Updated Dec 8, 2022Dec 8, 2022
    • This repository's sole purpose is to verify that secrets may indeed be limited to a selected branch
      0000Updated Jun 14, 2022Jun 14, 2022
    • sdust

      Public
      Rust
      MIT License
      0000Updated May 5, 2022May 5, 2022
    • template-python

      Public template
      Template Python repository
      Makefile
      MIT License
      0003Updated 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
      1.9k000Updated 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
      102000Updated Jul 2, 2021Jul 2, 2021
    • Terraform module to create an Elastic Kubernetes (EKS) cluster and associated worker instances on AWS
      HCL
      Other
      4.4k000Updated 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
      26000Updated Apr 14, 2021Apr 14, 2021
    • Docker container for tseemann/shovill
      Dockerfile
      MIT License
      0000Updated Jan 31, 2021Jan 31, 2021
    • Docker container for the Unicycler hybrid assembler
      Dockerfile
      MIT License
      1201Updated Jan 31, 2021Jan 31, 2021
    • Public Dockerfiles
      Dockerfile
      MIT License
      0000Updated Jan 31, 2021Jan 31, 2021