Discovered public repositories for benedictpaten in the GitHub catalog.
Work on data models and APIs for graph structures that represent the human reference genome plus common human genetic variants. Includes mapping to a reference genome, and standardization of the mechanism for referring to variants.
Library for constructing pinch graphs and cactus graphs
Library of matching and ordering algorithms, used for "reference problem"
Prototype implementation of SQG parser in Python
Evaluation scripts for testing cactus progressive method
Scripts for evaluating a cactus reference genome
A home for various common but non-essential scripts for the cactus project
Benchmarking scripts for assessing assemblies, used in the Assemblathon 1 project
Library for Assemblathon 1 analysis scripts
Evolutionary transducer based method for aligning and reconstructing indel histories
Probabilistic consistency based aligner
Small general purpose library for C and Python with focus on bioinformatics.
Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)