FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments

Josiah Seaman; Richard J A Buggs

doi:10.3389/fgene.2020.00292

FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments

Front Genet. 2020 Apr 30:11:292. doi: 10.3389/fgene.2020.00292. eCollection 2020.

Authors

Josiah Seaman^{1

2}, Richard J A Buggs^{1

2}

Affiliations

¹ Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom.
² School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

Abstract

Researchers seldom look at naked genome assemblies: instead the attributes of DNA sequences are mediated through statistics, annotations and high level summaries. Here we present software that visualizes the bare sequences of whole genome assemblies in a zoomable interface. This can assist in detection of chromosome architecture and contamination by the naked eye through changes in color patterns, in the absence of any other annotation. When available, annotations can be visualized alongside or on top of the naked sequence. Genome alignments can also be visualized, laying two genomes side by side in an alignment and highlighting their differences at nucleotide resolution. FluentDNA gives researchers direct visualization of whole genome assemblies, annotations and alignments, for quality control, hypothesis generation, and communicating results.

Keywords: chromosome structural variants; comparative genomics; data visualization; genome alignment; genome assembly; genome browser; nucleotide visualization; space filling curves.