Rapid large-scale prokaryote pan genome analysis
SORMAS (Surveillance, Outbreak Response Management and Analysis System) is an early warning and management system to fight the spread of infectious diseases.
Finds SNP sites from a multi-FASTA alignment file
Mathematical Modeling of Infectious Disease Dynamics
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
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Unified COVID-19 Dataset
Antimicrobial Resistance Identification By Assembly
Get assembly statistics from FASTA and FASTQ files
Infectious Disease Sequencing Platform
Simulation, visualization, and inference of individual level infectious disease models with Julia
Python3 scripts to manipulate FASTA and FASTQ files
de novo virus assembler of Illumina paired reads
Improve the quality of a denovo assembly by scaffolding and gap filling
Python Virus Simulation: Model and visualize epidemic spread using mathematical models (SIR) and interactive dashboards.
Domain-Specific Modeling for Epidemiology
Predict plasmids from uncorrected long read data
R Package for individual based epidemiological models
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