# ChromoMapper: a new tool to quickly compare large genome assemblies

## TL;DR

ChromoMapper is a new tool that helps scientists quickly compare large genome assemblies by visualizing similarities and differences.

## Contribution

The novel contribution is a tool that visualizes chromosomal alignment regions and differences between genome assemblies using QUAST and similar data.

## Key findings

- ChromoMapper identifies and displays similarities and differences between genome assemblies.
- It highlights collinearity, inconsistencies, and repeated regions in assemblies.
- The tool is available online and through Zenodo for public use.

## Abstract

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.

Here we present ChromoMapper, a new tool which scans the output from QUAST, 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.

ChromoMapper is available at https://chromomapper.ceinge.unina.it/ and via Zenodo (https://doi.org/10.5281/zenodo.16778863).