benedictpaten/toil
Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.
Evolutionary transducer based method for aligning and reconstructing indel histories
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Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
UCSC Nanopore
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.