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FOI-Bioinformatics / flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
GNU General Public License v3.0
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Add - to fit bracken names and nodes format #25

Closed davve2 closed 4 years ago

davve2 commented 4 years ago

To add on to this as well, here are the two lines indicating the format for the nodes.dmp & names.dmp files: https://github.com/DerrickWood/kraken2/blob/master/scripts/build_rdp_taxonomy.pl Lines 55 & 56 This is the format that Kraken & Bracken specifically work with.

Originally posted by @punnettsun in https://github.com/FOI-Bioinformatics/flextaxd/issues/16#issuecomment-717608801

davve2 commented 4 years ago

Thanks for your comments! I find adding a - in an empty column as a strange solution as it is not the standard NCBI format, but also an easy one to fix.

I´ve never used bracken downstream so far, which is why I haven´t noticed this error as it doesn´t occur while using kraken2 alone!