John Lees

seer. sequence element (kmer) enrichment analysis

23andme-impute. Scripts and advice to run IMPUTE2 on 23 and me raw data

bioinformatics. Utilities written for bioinformatics

which_tree. Testing of phylogenetic inference methods

tajima-D. calculates tajima's D from bcftools query input

rapidnj. Code for rapidNJ by Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen.

efficient-bge. scripts and methods for fast bacterial genomic epidemiology

R_plots. Some scripts to create plots in R

pyseer. SEER, reimplemented in python

PopPUNK-web. Web version of PopPUNK

paired-samples. Scripts and plots used for 'Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis'

config. Config files stored in ~

cuda_rng_benchmarking. Benchmarking the RNG in dust against curand

PopPUNK-scripts. Scripts used to help produce extra analysis for the PopPUNK manuscript

genometrackr_access. Downloading data from NCBI Genometrackr