sequana_coverage is a standalone application that reports genomic regions of interest (ROIs) which are significantly over- or under-represented in high throughput sequencing data. Thanks to HTML reports, is allows users to browse the detected ROI. This tool can be used to detect CNVs or deleted regions from a few bases to several kB. It was published in 2018 in GigaScience (, giy110, https://doi.org/10.1093/gigascience/giy110). Please see the online article for details.
Here below is a snapshot of a CNV detectd within a bacterial genome. The algorithm implemented within sequana_coverage can be very precise and determined the starting and ending position with high confidence.
This work was done within the Biomics Platform and is part of the Sequana software