Sars Cov 2 Python Packages

sc2ts

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

seirsplus

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

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.

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

pyncov

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

sars2seq

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

python-outbreak-info

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

covid19-py

🦠See COVID-19 data from the command line

covsonar

A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.

mediamaker

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

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.