infectious-diseases

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

Simulating epidemics using Python

Domain-Specific Modeling for Epidemiology

Predict plasmids from uncorrected long read data

Multilocus sequence typing by blast using the schemes from PubMLST