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DepthKopy calculates the mean CN for Duplicated BUSCO genes and assigns a True/False Duplicate rating accordingly. A future release will extend this functionality to other gene/feature families. Please reply here or get in touch if this is of interest and you want to help test the feature.

DepthKopy parallelises processing by extracting depths for one sequence at a time. This can cause a massive blowout of temporary files for highly fragmented genomes. The next update will include an option to chunk up the input by size to some extent instead.

Applying DepthKopy to short-read data has revealed a bug in DepthKopy that can give shifted results when there is a big chunk of zero coverage at the start of a sequence. This will be fixed in the next update.

DepthKopy was developed using high-quality assemblies with good long-read coverage, so this bug escaped detection. Sorry!