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marbl / Krona

Interactively explore metagenomes and more from a web browser.
https://github.com/marbl/Krona/wiki
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SARS-COV2 #158

Open khoriba opened 3 years ago

khoriba commented 3 years ago

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?

nankaiwolf commented 3 years ago

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 commented 3 years ago

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

khoriba commented 3 years ago

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

nankaiwolf commented 3 years ago

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.

khoriba commented 3 years ago

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