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abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

alignio_convertformat

Convert DNA alignments between BioPython-supported formats.

arbow

Cultivate your multiple sequence alignments to get better trees

babykraken

bohra

A pipeline for bioinformatics analysis of bacterial genomes

boobook

a Python tool to count RNA-seq reads mapping to genomic features

coreugate

a cgMLST pipeline tool for public health

covid-venn

Shiny app for creating Venn diagrams of SARS-CoV-2 variant/lineage mutations.

covid19-paper

Data for publications related to Victorian SARS-CoV-2 genomic epidemiology

cpe-paper

Data for publications related to Victorian CPE surveillance and genomic epidemiology

create_krakendb

A pipeline to make an MDU kraken DB

dcompressee

A small library to return temporary decompressed files when one needs them.

demo

Anders testing

emmtyper

emm Automatic Isolate Labeller

github-watch

havic

Detect Hepatitis A Virus Infection Clusters

hicap

👋🎓 in silico typing of the H. influenzae cap locus

himal_scripts

Some scripts for MDU data

join_mlst_or_abricate_tables

Joins nullabor mlst2.tab files into mlst2 super table (csv), or resistome.csv files into super resistome table (csv)

kovid-trees-nf

Fast trees for SARS-CoV-2

kristy_helper_scripts

Some helpful (or not) scripts for wrangling MDU data

lissero

In silico serotype prediction for Listeria monocytogenes

make_prokka_safe

Make your read set prokka safe before running Nullarbor

mdu-pytools

Small tools/scripts written in python

mdu-tools

Scripts for dealing with internal MDU filesystem structure

meningotype

In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis

ngmaster

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)

nullarbor-reads

Make an input file for nullarbor under diverse conditions.

pairwise_snp_differences

An R script to summarise pairwise SNP differences among groups of samples.

pando

With a file of isolate IDs as input, compile all results (abricate, kraken, mlst) into a single table and infer an NJ tree using the alignment-free Andi phylogenomic software.