Microbiological Diagnostic Unit Public Health Laboratory (@MDU-PHL)
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MDU-PHL

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  • Stars
    star
    157
  • Global Org. Rank 46,060 (Top 15 %)
  • Registered almost 10 years ago
  • Most used languages
    Python
         66.7 %
    HTML
         14.3 %
    Nextflow     9.5 %
    R
         4.8 %
    Perl
         4.8 %
  • Location 🇦🇺 Australia
  • Country Total Rank 2,868
  • Country Ranking
    Nextflow     2
    Perl
         202
    R
         442
    Python
         490
    HTML
         932

Top repositories

1

abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes
Python
65
star
2

bohra

A pipeline for bioinformatics analysis of bacterial genomes
Nextflow
18
star
3

meningotype

In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis
Python
10
star
4

pango-collapse

app to collapse Pango lineages for reporting
Python
8
star
5

LisSero

In silico serotype prediction for Listeria monocytogenes
Python
7
star
6

arbow

Cultivate your multiple sequence alignments to get better trees
Python
6
star
7

ngmaster

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
Python
5
star
8

kovid-trees-nf

Fast trees for SARS-CoV-2
Nextflow
5
star
9

pairwise_snp_differences

An R script to summarise pairwise SNP differences among groups of samples.
R
3
star
10

Coreugate

a cgMLST pipeline tool for public health
Python
3
star
11

tbtamr

AMR inference for Mtb - cousin to abriTAMR
HTML
3
star
12

mdu-tools

Scripts for dealing with internal MDU filesystem structure
Perl
2
star
13

babykraken

2
star
14

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
Python
1
star
15

pango-watch

HTML
1
star
16

create_krakenDB

A pipeline to make an MDU kraken DB
1
star
17

who2tbp

A script to convert WHO MTB resistant variants to a format that can be ingested by TBProfiler
Python
1
star
18

nullarbor-reads

Make an input file for nullarbor under diverse conditions.
Python
1
star
19

COVID19-paper

Data for publications related to Victorian SARS-CoV-2 genomic epidemiology
1
star
20

salmonella_typing

Salmonella serotyping at MDU
Python
1
star
21

rezzie

A small library for accessing resources and data shipped with your package without using the pkg_resources API.
Python
1
star
22

join_mlst_or_abricate_tables

Joins nullabor mlst2.tab files into mlst2 super table (csv), or resistome.csv files into super resistome table (csv)
Python
1
star
23

troika

A pipeline implementing TB-profiler for detection and reporting of AMR in Mtb for public health
HTML
1
star
24

mdu-pytools

Small tools/scripts written in python
Python
1
star