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.
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
Unified COVID-19 Dataset
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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
Improve the quality of a denovo assembly by scaffolding and gap filling
Simulating epidemics using Python
de novo virus assembler of Illumina paired reads
Domain-Specific Modeling for Epidemiology
Predict plasmids from uncorrected long read data
Multilocus sequence typing by blast using the schemes from PubMLST
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