René L. Warren

TL;DR: These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

TL;DR: HLAminer, a computational method for identifying HLA alleles directly from shotgun sequence datasets that circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.

TL;DR: NanoSim is introduced, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology and is expected to have an enabling role in the field and benefit the development of scalable next-generation sequencing technologies for the long nanopore reads.

TL;DR: ARCS is presented, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies and is expected to have broad utility in harnessing the barCoding informationcontained in linked read data for connecting high‐quality sequences in genome assembly drafts.

TL;DR: Sealer is an automated finishing application that uses the succinct Bloom filter representation of a de Bruijn graph to close gaps in draft assemblies, including that of very large genomes, to have broad utility for finishing genomes across the tree of life.