MDU-PHL/COVID19-paper

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MDU-PHL/COVID19-paper

MDU-PHL

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

abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

bohra

A pipeline for bioinformatics analysis of bacterial genomes

meningotype

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

pango-collapse

app to collapse Pango lineages for reporting

LisSero

In silico serotype prediction for Listeria monocytogenes

arbow

Cultivate your multiple sequence alignments to get better trees

ngmaster

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

kovid-trees-nf

Fast trees for SARS-CoV-2

pairwise_snp_differences

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

Coreugate

a cgMLST pipeline tool for public health

tbtamr

AMR inference for Mtb - cousin to abriTAMR

mdu-tools

Scripts for dealing with internal MDU filesystem structure

babykraken

parseGenbanksExtractCDSsByGeneName

Takes a list of CDS gene names (whitespace separated) and extracts the genes from a list of genbank files (can do *.gbk files) and outputs a multi-fasta file for each CDS name

pango-watch

create_krakenDB

A pipeline to make an MDU kraken DB

who2tbp

A script to convert WHO MTB resistant variants to a format that can be ingested by TBProfiler

nullarbor-reads

Make an input file for nullarbor under diverse conditions.

salmonella_typing

Salmonella serotyping at MDU

rezzie

A small library for accessing resources and data shipped with your package without using the pkg_resources API.

join_mlst_or_abricate_tables

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

troika

A pipeline implementing TB-profiler for detection and reporting of AMR in Mtb for public health

mdu-pytools

Small tools/scripts written in python