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How to produce consensus genome

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  • How to produce consensus genome

    I have two sequences I wish to assemble to give a consensus genome. I am using Velvet assembler

    would this commandline be OK

    ./velveth conref_out 35 -fastq.gz -shortPaired -separate /Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/EN28FP.fq.gz //Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/EN28RP.fq.gz /Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/KN99aFP.fq.gz /Users/emmannaemeka/Desktop/QTL_ANALYSIS/Trimmomatic-0.36/KN99aRP.fq.gz

    were FP= forward paired RP= Reverse paired EN28= Sequence 1 KN99a= Sequence 2

    Thanks

  • #2
    For reference cross-posted: https://www.biostars.org/p/284783/

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