MDU-PHL/pango-collapse

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Language
Python
License
GNU General Publi...
Created about 2 years ago
Updated 8 months ago

MDU-PHL/pango-collapse

MDU-PHL

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app to collapse Pango lineages for reporting

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

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.

COVID19-paper

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

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