PyRank

Infectious Diseases Python Packages

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

Python3 scripts to manipulate FASTA and FASTQ files

3K 73 21
AlFontal
jp-idwr-db

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

2K 0 0
sanger-pathogens
ariba

Antimicrobial Resistance Identification By Assembly

1K 186 60
epispot
epispot-nightly

A tool for modeling infectious diseases.

1K 18 6
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.

948 0 1
sanger-pathogens
circlator

A tool to circularize genome assemblies

425 257 57
epispot
epispot

A tool for modeling infectious diseases.

405 18 6
sanger-pathogens
iva

Iterative Virus Assembler

331 58 19
quadram-institute-bioscience
albatradis

Comparative TraDIS analysis

222 9 4
andrewjpage
tiptoft

Predict plasmids from uncorrected long read data

180 41 10
nathangeffen
ziggie

Python package for infectious disease modelling

165 1 0
andrewjpage
plasmidpredictor

Predict plasmids from uncorrected long read data

152 41 10
raghavagps
fluspred

A bioinformatic-ware to predict the zoonotic host tropism of Influenza A virus.

116 3 1
sanger-pathogens
seroba

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

101 25 20