sap-phe-bioinformatics Goto Github PK

bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

bactopia

A flexible pipeline for complete analysis of bacterial genomes

chorus

Candida auris specific workflow for public health testing

ecoli_serotyping

In silico prediction of E. coli serotype

emm-typing-tool

Group A streptococci emm typing tool for NGS data

funphehr

A fungal assembly and annotation nextflow pipeline

legsta

🍗⭐ In silico Legionella pneumophila Sequence Based Typing

lissero

In silico serotype prediction for Listeria monocytogenes

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)

phesiqcal_-eyre-

A snakemake workflow for downstream processing of WGS

phet

Pipeline for Downstream processing of whole genome sequenced bacterial isolates

pyngstar

Python script to run NG-STAR typing on N. gonorrhoeae assemblies

seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

serocall

Pneumococcal serotype quantification using NGS reads

shigatyper

CFSAN Shigella Typing Pipeline

shigeifinder

Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies

sistr_cmd

SISTR (Salmonella In Silico Typing Resource) command-line tool

sonneityping

tbprofiler

Profiling tool for Mycobacterium tuberculosis to detect resistance and strain type from WGS data, adding in Family lineage information