ChromoMapper: a new tool to quickly compare large genome assemblies

Motivation: Quality assessment and assembly comparison are essential steps while assembling new genomes. Many tools for evaluating assemblies typically provide synthetic parameters representing assembly quality or overall features, while others provide long detailed files where it is not always easy to identify and visualize the regions of correspondence and difference among different chromosome assemblies. Results: , as well as other similar alignment description files, to quickly identify and display similarities and differences between the compared assemblies. It uses the information provided about aligned blocks, combined with additional annotations, to represent the main alignment regions at chromosomal or sub-chromosomal scale, highlighting similarities and collinearity between compared sequences, points of inconsistency, discontinuities, repeated regions and interruptions in the assembled sequences. Availability and implementation: is available at https://chromomapper.ceinge.unina.it/ and via Zenodo (https://doi.org/10.5281/zenodo.16778863).