Alvis- A New Tool for Alignment & Visualization of Contigs & Reads and Chimera Detection

Visualization of running alignments of reads and contigs facilitates easy analysis and is useful in presenting assembly results. Several tools such as Artemis, BLAST Web, Circos, and so on, exist. A new tool called Alvis is developed for easy alignment and visualization of contigs and reads [1]. It can also be used for chimera detection.

Alvis is a user-friendly command-line tool capable of generating visuals of common alignment tasks. It can generate four different kinds of diagrams and accepts the input in different formats including BLAST tabular, PAF format from minimap2, SAM files, PSL file, and MUMmer’s .coords and .tiling files. Users can also filter the alignments. Alvis highlights the potential chimeric contigs or reads in the output.

The visualization output of Alvis includes:

• alignment diagram,
• contig alignment diagram,
• coverage map diagram, and
• genome coverage diagram.

Alvis is written in Java with a simple command-line interface. It is platform-independent unless it consists of a Java Runtime Environment. Alvis is freely downloadable from Github.

For more information, read here.

References

1. Martin, S., Leggett, R.M. (2021). Alvis: a tool for contig and read ALignment VISualisation and chimera detection. BMC Bioinformatics 22, 124.