MDU-PHL/abritamr MDU-PHL/abritamr

  • Stars
    star
    65
  • Rank 473,702 (Top 10 %)
  • Language
    Python
  • Created about 5 years ago
  • Updated 3 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
MDU-PHL/abritamr
github

MDU-PHL

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

A pipeline for running AMRfinderPlus and collating results into functional classes

More Repositories

1

bohra

A pipeline for bioinformatics analysis of bacterial genomes
Nextflow
18
star
2

meningotype

In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis
Python
10
star
3

pango-collapse

app to collapse Pango lineages for reporting
Python
8
star
4

LisSero

In silico serotype prediction for Listeria monocytogenes
Python
7
star
5

arbow

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

ngmaster

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
Python
5
star
7

kovid-trees-nf

Fast trees for SARS-CoV-2
Nextflow
5
star
8

pairwise_snp_differences

An R script to summarise pairwise SNP differences among groups of samples.
R
3
star
9

Coreugate

a cgMLST pipeline tool for public health
Python
3
star
10

tbtamr

AMR inference for Mtb - cousin to abriTAMR
HTML
3
star
11

mdu-tools

Scripts for dealing with internal MDU filesystem structure
Perl
2
star
12

babykraken

2
star
13

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
14

pango-watch

HTML
1
star
15

create_krakenDB

A pipeline to make an MDU kraken DB
1
star
16

who2tbp

A script to convert WHO MTB resistant variants to a format that can be ingested by TBProfiler
Python
1
star
17

nullarbor-reads

Make an input file for nullarbor under diverse conditions.
Python
1
star
18

COVID19-paper

Data for publications related to Victorian SARS-CoV-2 genomic epidemiology
1
star
19

salmonella_typing

Salmonella serotyping at MDU
Python
1
star
20

rezzie

A small library for accessing resources and data shipped with your package without using the pkg_resources API.
Python
1
star
21

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
22

troika

A pipeline implementing TB-profiler for detection and reporting of AMR in Mtb for public health
HTML
1
star
23

mdu-pytools

Small tools/scripts written in python
Python
1
star