One Codex

rust-bfield

B-field implementation in Rust

needletail

Fast FASTX parsing and k-mer methods in Rust

finch-rs

A genomic minhashing implementation in Rust

taxonomy

Python and Rust library for loading, saving, and manipulating taxonomic trees

onecodex

Command line interface and Python client library for the One Codex API

sars-cov-2

SARS-CoV-2 variant calling and consensus assembly pipeline

chrononaut

A history mixin with audit logging, record locking, and time travel for FlaskSQLAlchemy

nim-bitarray

Bitarray implementation in Nim

mmap-bitvec

Rust implementation of a mmap-based bit vector

docker-onecodex-notebook

Docker image with a Jupyter notebook environment for embedded use on One Codex

docker-unicycler

Docker container for the Unicycler hybrid assembler

assembly-annotation-tools

onecodex-uploader

(DEPRECATED) GUI uploader for the One Codex site

limit-secrets-test

This repository's sole purpose is to verify that secrets may indeed be limited to a selected branch

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

altair_saver

Altair extension for saving charts in a variety of formats.

bacillus-anthracis-panel

Description of One Codex B. anthracis marker panel design and testing

docker-shovill

Docker container for tseemann/shovill

flask-limiter

rate limiting extension for flask applications

flask-login

Flask user session management.

flask-smorest

DB agnostic framework to build auto-documented REST APIs with Flask and marshmallow

genome_portal_api

Python package to access and download data from the ATCC Genome Portal (https://genomes.atcc.org/)

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

laptop

A shell script to set up a macOS laptop for web and mobile development.

metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

potion

Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine

public-dockerfiles

Public Dockerfiles

sdust

template-python

Template Python repository

terraform-aws-eks

Terraform module to create an Elastic Kubernetes (EKS) cluster and associated worker instances on AWS