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Chapter for Statistical Population Genetics
A reimplementation of Hudson's classical ms simulator for modern data sets.
Example of tracking the ARG during forward simulations. Implementation is a Python package using fwdpp, fwdpy11, msprime, and pybind11.
Specifications of SAM/BAM and related high-throughput sequencing file formats
A tester for the htsget API.
A demo of the Python C API for CodeMonkeys
Python client for GA4GH htsget protocol
Conda recipes for the bioconda channel.
A conda-smithy repository for gsl.
Genome inference from a population reference graph
Work on data models and APIs for Genomic data.
A reference implementation of the APIs defined in the schemas repository.
Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Code used for running my HTPC
Comparisons of simulators for the msprime paper
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Efficient coalescent simulations in a spatial continuum
Protocol Buffers - Google's data interchange format
A compliance test suite for the APIs defined in the schemas repository.
Simulations of ancestral waves for the continuum, Wright-Fisher and Moran models.
A genotype query interface.
An example Python package, which simulates Kingman's coalescent.
Build a Jekyll blog in minutes, without touching the command line.
Experimental C client library for the GA4GH API.
An accurate coalescent simulator for genome-scale sequences
Cortex on steroids: for larger populations with better assembly
Experimental tool to convert Variant Call Format files to Apache Avro
EMR training repo