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    60 repositories

    • onecodex

      Public
      Command line interface and Python client library for the One Codex API
      Python
      •
      MIT License
      •12•23•28•3•Updated Nov 22, 2024Nov 22, 2024

    • 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 Nov 15, 2024Nov 15, 2024

    • needletail

      Public
      Fast FASTX parsing and k-mer methods in Rust
      Rust
      •
      MIT License
      •21•174•13•2•Updated Nov 1, 2024Nov 1, 2024

    • taxonomy

      Public
      Python and Rust library for loading, saving, and manipulating taxonomic trees
      Rust
      •
      MIT License
      •3•35•8•0•Updated Nov 1, 2024Nov 1, 2024

    • rust-bfield

      Public
      B-field implementation in Rust
      Rust
      •
      Apache License 2.0
      •4•204•4•0•Updated May 23, 2024May 23, 2024

    • finch-rs

      Public
      A genomic minhashing implementation in Rust
      Rust
      •
      MIT License
      •8•93•15•2•Updated Jan 15, 2024Jan 15, 2024

    • chrononaut

      Public
      A history mixin with audit logging, record locking, and time travel for FlaskSQLAlchemy
      pythonflaskpostgressqlalchemyflask-sqlalchemy
      Python
      •
      MIT License
      •4•17•3•2•Updated Jan 8, 2024Jan 8, 2024

    • 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•24•1•1•Updated Sep 18, 2023Sep 18, 2023

    • potion

      Public
      Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine
      Python
      •
      Other
      •51•0•0•1•Updated Aug 3, 2023Aug 3, 2023

    • flask-login

      Public
      Flask user session management.
      Python
      •
      MIT License
      •803•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
      •33•0•0•0•Updated Jul 19, 2023Jul 19, 2023

    • flask-limiter

      Public
      rate limiting extension for flask applications
      Python
      •
      MIT License
      •126•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
      •4•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
      •73•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
      🔎 💊 Mass screening of contigs for antimicrobial and virulence genes
      Perl
      •
      GNU General Public License v2.0
      •92•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
      •4.1k•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
      •17•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

    • bacillus-anthracis-panel

      Public
      Description of One Codex B. anthracis marker panel design and testing
      HTML
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated Dec 14, 2020Dec 14, 2020

    • nim-bitarray

      Public
      Bitarray implementation in Nim
      Nim
      •
      MIT License
      •4•10•1•0•Updated Dec 14, 2020Dec 14, 2020

    • onecodex-uploader

      Public
      (DEPRECATED) GUI uploader for the One Codex site
      Python
      •
      MIT License
      •1•1•0•0•Updated Dec 14, 2020Dec 14, 2020

    • homebrew-bio

      Public
      🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
      Ruby
      •
      Other
      •120•0•0•0•Updated Feb 21, 2020Feb 21, 2020