Background

I joined the lab in February 2010. My current focus is support of the NCBI variant calling processing pipeline for the 1000 Genomes project. I am personally interested in all aspects of genomic observation and variation.

Since joining I have specifically focused on developing adapting the lab’s core variant detection algorithm (GigaBayes) to non-uniform copy number and abstractly-defined alleles. The result of this work is FreeBayes, a variant detection system which combines these algorithmic developments with substantial performance enhancements.

In addition to this work I support the lab as a programmer and technical associate in a number of related bioinformatics software projects:

fastahack - utilities for indexing and sequence extraction from FASTA files vcflib - a C++ library for parsing and manipulating VCF files. phred.py - phred score manipulation in python jvcf - Joint Variant Call Format – JSON notation for genetic variant annotation multichoose - C++ library containing a generic function to generate multiset combinations (n multichoose k) from vectors of any type. parallelizer - scripts to simplify trivial parallelization of data processing software fasta-utilities - python scripts for FASTA file manipulation. A full list of my public repositories can be found on my user page on github.