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SARS-COV2

Open khoriba opened this issue 4 years ago • 5 comments

Hi, I analyzed metagenome data including the SARS-COV2 genome. I tried to browse this data, but SARS-COV2 was expressed as "other Root" by Krona. Is there anything I can do for browsing this virus in Krona chart?

khoriba avatar Mar 25 '21 14:03 khoriba

I tried this issue. I use "kreport2krona.py" to convert kraken2 report to krona file, and use "ktImportText" to convert krona file to html file. Then open html in browser.

nankaiwolf avatar Mar 25 '21 15:03 nankaiwolf

The kraken2 database was built by NCBI database, so the SARS-CoV2 genome can be aligned by kraken2.

nankaiwolf avatar Mar 25 '21 15:03 nankaiwolf

I also used Kraken2, but Krona didn't translate the taxonomy id of SARS-COV2.

khoriba avatar Mar 25 '21 16:03 khoriba

I updated the (almost) latest NCBI database in February, and have the SARS-CoV2 genome collected in. However, I downloaded the database not by kraken2-build, but used Kraken_db_install_scripts (https://github.com/mw55309/Kraken_db_install_scripts). Changed some codes, of course. And "kreport2krona.py" is in https://github.com/jenniferlu717/KrakenTools, very useful, highly recommended.

nankaiwolf avatar Mar 25 '21 17:03 nankaiwolf

Thanks! I got a Krona chart including "Severe acute respiratory syndrome coronavirus 2".

khoriba avatar Mar 25 '21 23:03 khoriba