Dear Wei Zhang,
I hope this message finds you well. I am researcher at CSIR-IGIB, currently using PathogenTrack for pathogen quantification and find the tool highly effective for my analysis. I have a question regarding the classify step in the workflow:
In step 5, reads are classified using Kraken2 via the following command:
"python PathogenTrack.py classify --project_id test/ --kraken_db /path/to/minikraken_8GB_20200312/ "
However, I would like to use Bracken files instead of the Kraken2 database for this step. Could you please advise on whether PathogenTrack supports Bracken files directly or suggest any modifications to the workflow that would allow me to integrate Bracken?
Thank you for your time and for developing such an insightful tool. I look forward to your guidance.
Best regards,
Jyoti Soni
Dear Wei Zhang,
I hope this message finds you well. I am researcher at CSIR-IGIB, currently using PathogenTrack for pathogen quantification and find the tool highly effective for my analysis. I have a question regarding the classify step in the workflow:
In step 5, reads are classified using Kraken2 via the following command:
"python PathogenTrack.py classify --project_id test/ --kraken_db /path/to/minikraken_8GB_20200312/ "
However, I would like to use Bracken files instead of the Kraken2 database for this step. Could you please advise on whether PathogenTrack supports Bracken files directly or suggest any modifications to the workflow that would allow me to integrate Bracken?
Thank you for your time and for developing such an insightful tool. I look forward to your guidance.
Best regards,
Jyoti Soni