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

sars-cov-2

SARS-CoV-2 variant calling and consensus assembly pipeline

onecodex

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

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