(New in 2014) Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Combined they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees.

Genome Assembly and Analysis with Optical Restriction Maps

Optical Mapping Data as a Guide for Genome Assembly

Genome assembly -- the task of reconstructing a genome from the small fragments of DNA that can be sequenced by modern technologies -- is a difficult computational problem, in no small part due to the fact that the shotgun sequencing process cannot preserve the long-range structure of the genome being assembled. Optical mapping is a genomic technology, pioneered by David Schwartz, which can map the location of restriction sites along a genomic chromosome. Thus, optical mapping provides a long-range sparse representation

Principal Investigators

Students and Postdoctoral researchers:


iMetAMOS is an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. iMetAMOS is available as a workflow within the metAMOS package starting with version 1.5.

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