Sars Cov 2 Python Packages

dna-decode

Deterministic, interpretable genome→phenotype decoder: calls antibiotic/antiviral/antifungal resistance from DNA + names the exact genes/mutations driving each call. Spans bacteria, M. tuberculosis, fungi, HIV-1 & SARS-CoV-2 — independently validated on FREE measured wet-lab labels (EBI AMR Portal, Stanford HIVDB). Not a clinical tool.

relecov-tools

set of helper tools for the assembly of the different elements in the RELECOV platform (Spanish Network for genomic surveillance of SARS-Cov-2) as data download, processing, validation and upload to public databases, as well as analysis runs and database storage.

seirsplus

Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing.

sc2ts

ARG inference and analysis utilities for pandemic-scale SARS-CoV-2 data

pyross

PyRoss: inference, forecasts, and optimised control of epidemiological models in Python. github.com/rajeshrinet/pyross

bioexplorer

The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration

covid19-py

Track the COVID-19 data in the word from the command line

sars2seq

A Python library and command-line scripts for working with SARS-CoV-2 sequences

pyncov

Flexible mechanistic epidemiological model to learn and predict the spread of COVID-19

python-outbreak-info

Python interface to Outbreak.info, powered by GISAID

covsonar

A database-driven system for handling genomic sequences and screening genomic profiles.

mediamaker

Media Maker Python SDK for Blue Brain BioExplorer

multisub

Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

python-outbreak-data

Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info