A tool to circularize genome assemblies

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

Antimicrobial Resistance Identification By Assembly

Python3 scripts to manipulate FASTA and FASTQ files

de novo virus assembler of Illumina paired reads

Simulating epidemics using Python

Predict plasmids from uncorrected long read data

Assembling the cause of phenotypes and genotypes from NGS data

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

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

Order and orientation of complete bacterial genomes

A multivariate multi-step LSTM forecasting model for tuberculosis incidence with model explanation

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

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

A tool for modeling infectious diseases.

Mycobacterial pipeline

IDseq infectious disease command-line interface

Python SIR-x model implementation

Based on labeled data, multi-class and multi-label scoring of outbreak detection, annotation or prediction algorithms.

Prediction infectious strains of Influenza A virus for human