ChromoMapperWeb: evaluate genome alignments and track assembly steps within an interactive graphic environment

Rapid quality assessment and multiple assembly comparison are essential steps while assembling new genomes or re-sequencing known ones. Many available tools used for assembly evaluation produce global metrics, representing assembly quality or overall features, most of them working as command line tools that typically act on large data files and produce long detailed result files, where it is not always easy to identify regions of similarity or difference among different chromosome assemblies. ChromoMapperWeb is a new web tool that takes as input nucmer or QUAST output files, quickly identifies similarities and differences between the compared assemblies, and displays them using both table visualizations and pre-arranged or custom graphics. Graphical displays are interactive and allow progressive zoom levels which, in a few steps, move from full genome to very enlarged views, where even small alignment blocks are easily identified. The program, freely accessible through the web server https://chromomapperweb.ceinge.unina.it/, provides an easy-to-use graphical interface, used for experiment planning and interactive evaluation of the results, which include tables and graphical representations of whole genomes, chromosomes, or single blocks.