We now need more than ever to make genome analysis more intelligent. We need to read,
analyze, and interpret our genomes not only quickly, but also accurately and efficiently …

Long-read-only bacterial genome assemblies usually contain residual errors, most
commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix …

While long-read sequencing allows for the complete assembly of bacterial genomes, long-
read assemblies contain a variety of errors. Here, we present Trycycler, a tool which …

Long nanopore reads are advantageous in de novo genome assembly. However, nanopore
reads usually have broad error distribution and high-error-rate subsequences. Existing error …

Population-level comparisons of prokaryotic genomes must take into account the substantial
differences in gene content resulting from horizontal gene transfer, gene duplication and …

Many applications of text generation require incorporating different constraints to control the
semantics or style of generated text. These constraints can be hard (eg, ensuring certain …

Motivation Recent advances in sequencing technologies promise ultra-long reads of∼ 100
kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs …

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies
typically requires resource-intensive error-correction and consensus-generation steps to …

The fundamental challenge of multi-sample structural variant (SV) analysis such as merging
and benchmarking is identifying when two SVs are the same. Common approaches for …

Genome sequence analysis has enabled significant advancements in medical and scientific
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …