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amr-catalogue-demo

A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR catalogues

applymask

Apply mask to fasta file

arboreta

bovtb-nf-docker

Updated BovTB-nf (https://github.com/ellisrichardj/BovTB-nf) with docker function

bugflow_dsl2

catdocs

Documentation for Scalable Pathogen Pipeline Platform (SP3)

catsgo

Command client of SP3 for fetch, run and download.

catsup

pre-processing and upload module for SP3

cdiff_reporting

clockwork

CRyPTIC data processing pipelines

collaborative_github_exercise

Copied from https://github.com/RSE-Sheffield/collaborative_github_exercise with thanks!

compasscompact

A compact version of Oxford Compass (Complete Pathogen Analysis Software Solution)

crumpitmanagerapis

flanker

Gene-flank analysis tool

flye_medaka_workflow

fn5

SNP matrix generation with caching to disk to allow fast reloading

forest_filter

Using random forest classfiers to filter SNP calls

genomicdiversitypaper

Scripts for "Genomic diversity affects the accuracy of bacterial SNP calling pipelines"

gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

gpas-tb-ci-testing

Automated end-to-end testing of the GPAS TB pipeline

gpas_adb

GPAS Autonomous Database

gpas_ena_download

For downloading ENA samples and making them available to the GPAS pipeline

gpas_local_db

Database to hosted locally in the hospital, holding GPAS sourced data plus others

gramnegmmm

grumpy

Re-implementation of gumpy in rust for speed

gumpy

Genetics with numpy

gumpy-tutorial

Simple tutorial using a jupyter notebook to walkthrough how to use gumpy

illumina_snippy_workflow

labbox_backend

The backend files for the LabBox application

labbox_frontend

The front-end for the LabBox application