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…y DB; don't run Bakta annotation if all proteins were found in auxiliary DB Some hypotheticals might be filtered out during the final stage of the pipeline. To avoid computationally expensive alignment of such proteins, add all CDS features, whether they were marked as pseudogenes or not, to the auxiliary database. The proteins that overlap with RNA features are added to the auxiliary database for the same reason; Filter channel with proteins not found in auxiliary DB based on the FASTA entries number - if empty, don't run Bakta annotation processes.
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Implemented an interface to save the CDS annotation obtained upon pipeline completion in a shareable format (JSON file). Additionally, the generated index can be reused for subsequent runs to bypass Bakta annotation and speed up the computation. The pangenome index can therefore be published and shared between users annotating large datasets of related genomes.