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  • bacterial consensus sequence reference guided assembly

    Hello,

    I'm trying to generate a consensus sequence, for a bacterial genome, for a reference guided assembly. I've aligned the reads against the reference using Novoalign with SAM output.

    I've been playing around with trying to get SAMTOOLS to generate the consensus for me. I'm aware of the samtools.pl pileup2fq option, however, I'm not sure if I can make a pileup file for a single chromosome. Pileup with the -c option automatically assumes you have a diploid organism.

    Does anyone know if you can force SAMTOOLS to do what I want to do? For instance, what would you do if you wanted to generate the consensus sequence for a resequencing project for the human Y chromosome?

    Any suggestions greatly appreciated...

    Many thanks,

    Kerensa.

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