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lauterbur / Flex-sweep

Versatile tool for detecting selective sweeps with a variety of ages, strengths, starting allele frequencies, and completeness.
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bacterial genome? #12

Open jianshu93 opened 8 months ago

jianshu93 commented 8 months ago

Dear team,

Just wonder how I can use this tools for bacterial genomes since bacterial genomes are completely different, model should also be very different.

Thanks,

Jianshu

lauterbur commented 8 months ago

Hi Jianshu,

You're correct, bacterial genomes would be very different, and at the moment FlexSweep is only set up to run on diploid genomes. There are a few bacteria-specific tools you could try, including SweepCluster https://link.springer.com/article/10.1186/s12859-021-04533-6 and SINCOPA https://www.biorxiv.org/content/10.1101/2023.03.16.533065v1.abstract but I can't speak to the quality of these methods.

Best, Elise

On Sat, Mar 16, 2024 at 4:23 PM Jianshu_Zhao @.***> wrote:

Dear team,

Just wonder how I can use this tools for bacterial genomes since bacterial genomes are completely different, model should also be very different.

Thanks,

Jianshu

— Reply to this email directly, view it on GitHub https://github.com/lauterbur/Flex-sweep/issues/12, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABTKUNJ7WCR4UPENHD23C5DYYTH6LAVCNFSM6AAAAABEZV4Y36VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4TAMZTHE4DOMQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>