Wtdbg2: Parameter -g setting problem

17863952296 commented 2 years ago

when I run the following command: wtdbg2 -x ont -g 100m -t 16 -i ../food_bac_filtered/Cy_nano_nofood_filtered.fastq -fo Cy_nano_100m wtdbg2 -x ont -g 150m -t 16 -i ../food_bac_filtered/Cy_nano_nofood_filtered.fastq -fo Cy_nano_150m wtdbg2 -x ont -g 200m -t 16 -i ../food_bac_filtered/Cy_nano_nofood_filtered.fastq -fo Cy_nano_200m wtpoa-cns -t 16 -i Cy_nano_100m.ctg.lay.gz -o Cy_nano_100m.ctg.fa wtpoa-cns -t 16 -i Cy_nano_150m.ctg.lay.gz -o Cy_nano_150m.ctg.fa wtpoa-cns -t 16 -i Cy_nano_200m.ctg.lay.gz -o Cy_nano_200m.ctg.fa output results: The larger the -g parameter is set, the larger the final genome size (Cy_nano_XXX.ctg.fa) result is How do I determine the actual genome size of a species?(Denovo assemble: I don't know the genome size)

ruanjue commented 2 years ago

-g and -X are used together to select enough reads. When genome size is unknown, just set -g to a large enough number.

17863952296 commented 2 years ago

font{
    line-height: 1.6;
}
ul,ol{
    padding-left: 20px;
    list-style-position: inside;
}

    Thank you for your reply! 
    Best regardsZiguang Deng

                ***@***.***

---- Replied Message ----

     From 

        Jue ***@***.***>

     Date 

    9/26/2022 08:55

     To 

        ***@***.***>

     Cc 

        ***@***.***>
        ,

        ***@***.***>

     Subject 

          Re: [ruanjue/wtdbg2] Wtdbg2: Parameter -g setting problem (Issue #247)

-g and -X are used together to select enough reads. When genome size is unknown, just set -g to a large enough number.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

ruanjue / wtdbg2

Wtdbg2: Parameter -g setting problem #247