PyRank

Infectious Diseases Python Packages

Python packages with the GitHub topic infectious-diseases. Sorted by monthly downloads, with stars and forks.
sanger-pathogens
pyfastaq

Python3 scripts to manipulate FASTA and FASTQ files

4K 73 21
AlFontal
jp-idwr-db

Self-updating wrangled database of Japanese infectious disease surveillance data from NIID IDWR.

2K 0 0
malkreide
bag-health-mcp

MCP server for Swiss Federal Office of Public Health (BAG) — infectious disease surveillance, epidemiological data & wastewater signals via the IDD API. No auth required.

1K 0 0
epispot
epispot-nightly

A tool for modeling infectious diseases.

1K 18 6
sanger-pathogens
ariba

Antimicrobial Resistance Identification By Assembly

829 187 60
sanger-pathogens
circlator

A tool to circularize genome assemblies

551 258 57
sanger-pathogens
iva

de novo virus assembler of Illumina paired reads

272 58 18
epispot
epispot

A tool for modeling infectious diseases.

211 18 6
andrewjpage
tiptoft

Predict plasmids from uncorrected long read data

109 41 10
quadram-institute-bioscience
albatradis

Comparative TraDIS analysis

109 9 4
nathangeffen
ziggie

Python package for infectious disease modelling

94 1 0
sanger-pathogens
seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

85 27 20
raghavagps
fluspred

Prediction infectious strains of Influenza A virus for human

74 3 1
andrewjpage
plasmidpredictor

Predict plasmids from uncorrected long read data

37 41 10