Alvis: a tool for contig and read ALignment VISualisation and chimera detection

Samuel Martin, Richard M. Leggett

The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. The aligner outputs are often parsed automatically by scripts, but many kinds of analysis can benefit from the understanding that can follow human inspection of individual alignments. Additionally, diagrams are a useful means of communicating assembly results to others. We developed Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies. Alvis diagrams facilitate improved understanding of assembly quality, enable read coverage to be visualised and potential errors to be identified. Additionally, we found that splitting chimeric reads using the output provided by Alvis can improve the contiguity of assemblies, while maintaining correctness.