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augur

Pipeline components for real-time phylodynamic analysis

auspice

Web app for visualizing pathogen evolution

auspice.us

aws-cli

Universal Command Line Interface for Amazon Web Services

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics-with-python-cookbook-second-edition

Bioinformatics with Python Cookbook Second Edition, published by Packt

c-wap

SC2 variant detection and composition pipeline

cli

The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

cvxopt

CVXOPT -- Python Software for Convex Optimization

datrie

Fast, efficiently stored Trie for Python. Uses libdatrie.

dbvar

dbVar

deviva

Scripts for analyzing SARS-CoV-2 variants

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

faunadb-python

Python driver for FaunaDB

hisat-genotype

hisat2

Graph-based alignment (Hierarchical Graph FM index)

iq-tree

Efficient phylogenomic software by maximum likelihood

opencv

Open Source Computer Vision Library

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

pip

The Python package installer

psutil

Cross-platform lib for process and system monitoring in Python

rethinkdb

The open-source database for the realtime web.

spark-moderndataengineering

The source code for the book Modern Data Engineering with Apache Spark

sra-tools

SRA Tools

standard-raxml

vaquero

SARS-CoV-2 (Va)riant (Qu)antification in s(E)wage, designed for (Ro)bustness

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.