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42 search results found

Sormas Project ⭐ 289

SORMAS (Surveillance, Outbreak Response Management and Analysis System) is an early warning and management system to fight the spread of infectious diseases.

Epimodel ⭐ 236

Mathematical Modeling of Infectious Disease Dynamics

Rapid large-scale prokaryote pan genome analysis

Circlator ⭐ 193

A tool to circularize genome assemblies

Artemis ⭐ 191

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Snp Sites ⭐ 173

Finds SNP sites from a multi-FASTA alignment file

Covid 19_unified Dataset ⭐ 168

Unified COVID-19 Dataset

Gubbins ⭐ 154

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Antimicrobial Resistance Identification By Assembly

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

Pathogen.jl ⭐ 64

Simulation, visualization, and inference tools for modelling the spread of infectious diseases with Julia

Simulation_virus_covid 19 ⭐ 52

Simulating epidemics using Python

Kendrick ⭐ 46

Domain-Specific Modeling for Epidemiology

Python3 scripts to manipulate FASTA and FASTQ files

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

Pathogen Informatics Training ⭐ 38

de novo virus assembler of Illumina paired reads

Individual ⭐ 27

R Package for individual based epidemiological models

Czid Dag ⭐ 26

Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows.

Order and orientation of complete bacterial genomes

CIDO: Coronavirus Infectious Disease Ontology

Predict plasmids from uncorrected long read data

Gff3toembl ⭐ 20

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Epifilter ⭐ 18

Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional approaches

Sta427_sm4ide ⭐ 16

Repo for the course Statistical Methods in Infectious Disease Epidemiology at UZH

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

A tool for modeling infectious diseases.

Bio Tradis ⭐ 15

A set of tools to analyse the output from TraDIS analyses

Epidemiology ⭐ 14

CRAN Task View: Epidemiology

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

Saffrontree ⭐ 14

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

Lodestone ⭐ 11

Mycobacterial pipeline

Create Contact Matrices from Population Data

Emergent_epidemics_lab_ncov2019 ⭐ 9

An RShiny App for mapping nCoV2019 line list data

Idseq Cli ⭐ 7

IDseq infectious disease command-line interface

Sormas Angular ⭐ 7

Angular Frontend for the SORMAS project

Albatradis ⭐ 7

Comparative TraDIS analysis

Covid 19_piedmont ⭐ 7

COVID-19 Surveillance Data Modelling and Management Pipeline in Piedmont.

Infectious_disease_predictability ⭐ 6

Code and data for On the Predictability of Infectious Disease Outbreaks by SV Scarpino & G Petri

Incidence Estimation Tools

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