Dr. K. D. Murray's repositories
adapterremoval
AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
ANGStrom
Low coverage WGS data analysis package
ansible-jupyterhub
Ansible role to setup jupyterhub server
axe-experiments
Experiments showing the utility of Axe
Bio.jl
Bioinformatics and Computational Biology Infrastructure for Julia
BioSequences.jl
Biological sequences for the julia language!
BioSymbols.jl
A small package introducing nucleic and amino acid primitive types.
gbs-snakemake
Classes for GBS analysis using snakemake and stacks
InStruct
InStruct Bayesian MCMC Global Population Structure Analysis Program
knitr-examples
a collection of knitr examples
Mash
Fast genome and metagenome distance estimation using MinHash
mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing
mpg
Markovian sequence generator
NextGenMap
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.
parephase
5'PARE phasing
phd-presentations
PhD-related Presenations
popgen-notes
Population genetics notes
ringbauer-ibd
fork of https://git.ist.ac.at/harald.ringbauer/IBD-Analysis
sampler
Take photos of seeds/leavs in bags, automatically scanning in QR codes
snp-sites
Finds SNP sites from a multi-FASTA alignment file
sourmash
Compute and compare MinHash signatures for DNA data sets.
terastructure
TeraStructure is a new algorithm to fit Bayesian models of genetic variation in human populations on tera-sample-sized data sets (10^12 observed genotypes, i.e., 1M individuals at 1M SNPs). This package provides a scalable, multi-threaded C++ implementation that can be run on a single computer.
timecourse-sample-recorder
Records exact sampling times