Enhancement: Assigning multiple GPSC types to mixed (meta-genome) samples

[sreerampeela]

I have been utilizing PopPUNK for the assignment of GPSC clusters. Currently, I am working with nasopharyngeal metagenome data and aiming to identify multiple GPSC types present in a meta-genome, along with calculating their respective relative abundances. While there are established tools for identifying multiple serotypes from mixed samples (example: PneumoKITy), my specific interest lies in understanding whether PopPUNK incorporates features that facilitate the identification of multiple genotypes by mapping to an existing database, such as GPS_v6.

I wanted to know whether PopPUNK provides functionalities that align with my research needs.
Thank and Regards,
Sreeram Peela

[johnlees]

Hi Sreeram
Unfortunately we don't currently have this capability built into poppunk

[sreerampeela]

Dear Dr. John Lees, Thank you for the information. Thanks & Regards, Dr. Sreeram Peela, Ph.D. Medical Microbiology, Research Associate (ICMR), Department of Microbiology, JIPMER - Puducherry.

…

On Tue, Nov 14, 2023 at 3:07 PM John Lees ***@***.***> wrote: Hi Sreeram Unfortunately we don't currently have this capability built into poppunk — Reply to this email directly, view it on GitHub <#287 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOHU2H6M2UMWMGT3FMVSJIDYEM3VPAVCNFSM6AAAAAA7I6A7B2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBZHA2TMNBWGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>