infectious-diseases

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

Rapid large-scale prokaryote pan genome analysis

Mathematical Modeling of Infectious Disease Dynamics

Finds SNP sites from a multi-FASTA alignment file

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

A tool to circularize genome assemblies

Antimicrobial Resistance Identification By Assembly

Unified COVID-19 Dataset

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

Get assembly statistics from FASTA and FASTQ files

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

Infectious Disease Sequencing Platform

Python3 scripts to manipulate FASTA and FASTQ files

Simulating epidemics using Python

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

de novo virus assembler of Illumina paired reads

Domain-Specific Modeling for Epidemiology

Assembling the cause of phenotypes and genotypes from NGS data

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

Predict plasmids from uncorrected long read data

Please see https://github.com/chanzuckerberg/idseq-workflows for the latest version of IDseq workflows.

Multilocus sequence typing by blast using the schemes from PubMLST

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

Order and orientation of complete bacterial genomes

A set of tools to analyse the output from TraDIS analyses

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

A tool for modeling infectious diseases.

An RShiny App for mapping nCoV2019 line list data

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