Is it possible to get the Plus PF database on Kraken report so it correspond to that of Kraken2 please? If not any suggestion on how to report Kraken 2 output having used Plus PF database?
Index zone by BenLangmead is the source of those databases. Besides the latest versions of each database the site also offers downloads of all previous releases. Scroll down on the page to find those and compare the release dates to the date of the Galaxy version you are using.
Thanks for the response, Wolfgang.
Actually, I used Galaxy Europe, Kraken2, with the Plus PF database was used to assign taxonomy labels. What tool can I use to report Kraken2 output in order for me to classify and report the taxa of the ID?
Bracken can only take a Kraken report, and there is no Plus PF database on Kraken report. Will it be ok to use Plasmid database on Kraken Report, considering its a subset of Plus PF and target organisms are bacteria and archaea?
I will appreciate any input from your end please.
Regards,
Oluwatobi
The kraken2 tool has a “Create Report” section, in which you need to enable the “Print a report with aggregrate counts/clade to file” option. The resulting output can then be used with bracken.
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This was very helpful!!! Thanks a lot.