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

The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. 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.

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 the most common alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies. We found that splitting chimeric reads using the output provided by Alvis can improve the contiguity of assemblies, while maintaining correctness.

Authors: Samuel Martin, Richard M. Leggett