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sara-javadzadeh / FastViFi

Detect viral infection and integration sites on NGS input. Manuscript is in preparation.
GNU General Public License v3.0
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Use the whole exome sequencing? #8

Closed xiasijian closed 1 year ago

xiasijian commented 1 year ago

Hi, sara. I have no idea whether the software FastViFi is used for the NGS data from whole exome sequencing.

Best wishes.

xiasijian commented 1 year ago

image

Why does the kraken_datasets.tar.gz only contains hpv database?

sara-javadzadeh commented 1 year ago

Hi Sijian,

Yes, the kraken database including Kraken indexes are only available for HPV. What virus are you looking into? I can share databases for hepatitis B virus (HBV), hepatitis C virus (HCV) and Epstein–Barr virus (EBV). If you are looking into other viruses, I have some instructions on how to build custom kraken databases in the FastViFi readme. I'm available to answer any questions for building custom databases in case you had any trouble.

Best, Sara

xiasijian commented 1 year ago

Hi Sara,

Thanks for your reply. If it is convenient for you, can you share the database for Epstein–Barr virus (EBV)? If yes, I will be deeply grateful for you.

Best wishes Sijian

sara-javadzadeh commented 1 year ago

Sounds good. I'm compressing the EBV indexes. I will share a Google Drive link after compression and uploading.

xiasijian commented 1 year ago

Thanks a lot🌹

sara-javadzadeh commented 1 year ago

Hi Sijian, Here's the link for downloading Kraken indexes for EBV. Let me know if you had any problems when using it.

xiasijian commented 1 year ago

Great! Thanks for your efforts. 😊