flashton2003

parse_kraken2_report

Taxonomically informed parsing of kraken2 report output.

postcode_to_constituency

Quick hacky bit of code to convert postcode to UK electoral constituency.

OUCRU_bioinformatics_training

Materials for bioinformatics training at Oxford University Clinical Research Unit

sublime_blast

BLAST within sublime text

yamyam

Yet another mnemonic for yet another (typing) method

sra_upload

Package to write XML for uploading to NCBI

MinION_analysis

seqbox

local sequence management lightweight tools

stx_subtyping

bactopia

A flexible pipeline for complete analysis of bacterial genomes

blantyre_qrdr_typhi

covid_importations

end_tb_goal_assessment

flashton2003.github.io

gemucator

Genbank Mutation Locator: give it a mutation and it will tell you the location in the reference genome (and vice versa)

genotyphi

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

git_training

Git training repository - OUCRU Modelling and Stat teams

homoplasy_finder_scripts

light_phylogeny_practical

mlw_bioinformatics_pipelines

Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop

nanostat

Create statistic summary of an Oxford Nanopore read dataset

PHEnix

Public Health England SNP calling pipeline.

plotTree

query_ena_api

Small script to take an ENA accession and return the ERR

Salmonella_Isangi_Analysis_pipeline

Bioinformatics pipelines for Salmonella_Isangi genomics analysis

salmonella_qc

snakemake

tb_cartogram

A cartogram of estimated number of incident cases (all forms) of TB from WHO stats

yamyam-packages