search

bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
86 stars 17 forks source link

Enhancement: Assigning multiple GPSC types to mixed (meta-genome) samples #287

Open sreerampeela opened 7 months ago

sreerampeela commented 7 months ago

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 commented 7 months ago

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

sreerampeela commented 7 months ago

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 https://github.com/bacpop/PopPUNK/issues/287#issuecomment-1809856462, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOHU2H6M2UMWMGT3FMVSJIDYEM3VPAVCNFSM6AAAAAA7I6A7B2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBZHA2TMNBWGI . You are receiving this because you authored the thread.Message ID: @.***>