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antismash

antiSMASH

cecret

Nextflow workflow for our analysis of MonkeyPox

docker-builds

StaPH-B:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

freyja_summarizer

Creates a summary file from Freyja aggregated data (aggregated-freyja.tsv)

grandeur

UPHL's Reference Free Pipeline

heatcluster

Creates a heat map with an accompanying cluster map for a SNP matrix

kraken2

The second version of the Kraken taxonomic sequence classification system

legionella_pneumophila_genomics

This repository contains bioinformatics scripts and a Docker container to perform the in silico prediction of Legionella pneumophila serogroup from short read sequences using a supervised machine learning approach.

monkeypox

Nextstrain build for monkeypox virus

mutation_profile

Identify the sequence context flanking SNPs of interest and screen for potential profiles/signatures of interest

quaisar_singularity

QuAISAR pipeline for distribution

quaisar_singularity-1

Containerized version of QuAISAR

rasusa

seqtk

Toolkit for processing sequences in FASTA/Q formats

staphb_toolkit

Python Toolkit for using containerized programs in either Singularity or Docker

tbprofiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

vadr

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

vadr-build-tools

Scripts to assist in creating VADR model libraries