Recent research into structural variants (SVs) has established their importance to medicine
and molecular biology, elucidating their role in various diseases, regulation of gene …

Highlights•Next generation sequencing technologies have enabled large-scale genome
analyses.•Pan-genome analyses provide a framework for predicting and modeling genomic …

The MUMmer system and the genome sequence aligner nucmer included within it are
among the most widely used alignment packages in genomics. Since the last major release …

Reference genomes guide our interpretation of DNA sequence data. However, conventional
linear references represent only one version of each locus, ignoring variation in the …

Genomic differences range from single nucleotide differences to complex structural
variations. Current methods typically annotate sequence differences ranging from SNPs to …

Land plants evolved from charophytic algae, among which Charophyceae possess the most
complex body plans. We present the genome of Chara braunii; comparison of the genome to …

Whole-genome sequences are now available for many microbial species and clades,
however existing whole-genome alignment methods are limited in their ability to perform …

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

Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet
unsolved problem because of the non-contiguous transcript structure, relatively short read …

Dinoflagellates are important components of marine ecosystems and essential coral
symbionts, yet little is known about their genomes. We report here on the analysis of a high …