Visualization and Analysis Tools for Comparing Genomes and Assemblies

Advances in long-read sequencing has created a revolution in de novo genome assembly. Genome assemblies created using long reads are consistently about a thousand-fold more contiguous than assemblies based on next-generation sequencing alone. The appearance of highly contiguous genomes for related species is also opening up new avenues of in-depth comparative genomic analysis. Here we present two online software methods created to take advantage of long reads and the high-quality assemblies they allow us to produce.

We created Assemblytics to call variants from MUMmer genomic alignments. Assemblytics uses an advanced filtering algorithm to eliminate false positives due to repetitive sequence alignments, detects variants both within and between alignments on a contig, and categorizes the variants into 6 types by analyzing gaps and overlaps that hint at genomic repeats. By optimizing several algorithms in Assemblytics, we were able to make it freely available as a web application.

Ribbon is an online visualization tool that was created to visualize long-read and assembly alignments, inspired by complex variants in cancer. In addition to a reference-level overview, alignments of every read or contig can be shown as dot plots or intuitive new ribbon plots, bringing an unprecedented level of interactivity and clarity to genomic alignment analysis.

One of the major challenges in this era of fast advances in genomic sequencing technology is to take full advantage of new types of data. Here we present new methods that utilize high-contiguity genome assemblies enabled by advances in long-read sequencing.