This increase in Examination reviews parallels an increase in the number of minimizers as described by kraken2-inspect. Below is a desk evaluating the kraken2-inspect reports for db2 and db3.
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Exactly how much does the sequence duration deviate from your expected duration (or the amount variation is amid assemblies of a similar species). Similar for number of contigs/scaffolds. The sequence size, and number of contigs together with N50 and L50 Provide you an plan about the fragmentation.
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I did a Biopython 'modified' use of NCBI API, which can be all right, but nonetheless restrictive. There are no simple solutions in addition to downloading an enormous sequence database that has negligible makes use of further than "neighborhood blast". If you're able to ring fence the info you need with the download That may be a far better route, but thats a separate concern. $endgroup$
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