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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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Kraken2 Bacteria database missing certain taxa #733

Closed CompBioML closed 1 year ago

CompBioML commented 1 year ago

I created a custom bacterial database using the guide on github and tested it on a random set of reads from Blautia caecimuris and their were no matches. I checked out the full report and discovered its not even in its taxonomy. To double check if I made an error, I checked out the pre-made databases on https://github.com/BenLangmead/aws-indexes and found the same taxa was missing in its index. Their are multiple RefSeq sequences, so I was wondering why it wasn't present. Any help would be appreciated, thanks!

palatinate commented 1 year ago

next unless grep {$asm_level eq $_} ("Complete Genome", "Chromosome");

Only species with assembly level 'Complete Genome' or 'Chromosome' are included in the database. All available Blautia caecimuris assemblies are only on 'contig' level.

CompBioML commented 1 year ago

Yep this seems to be the solution, appreciate the help!