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  • Improving bacterial genome assembly


    Deall seqanswers community, hope you are all doing well.
    I have sequenced and assembled 8 bacterial genomes of the same species.
    The initial assembly was constructed using paired-end reads from a Miseq and was rather satisfying (to draw first conclusion).
    I also have long reads from PacBio of the same genomes and I would like to take advantage of both type of reads to improve my assembly and portray final conclusions with confidence. I am thinking of a scaffold approach whereby the Pacbio reads will be used to join contig. I would like you to guide me on a way forward.
    I am not comfortable with Unix command line

    Sincerely,

  • #2
    Several tools such as SPAdes support hybrid assembly using illumina and pacbio reads. Their test suggested illumina reads only generated 92 contigs, while illumina+pacbio generated 5 contigs for E coli K12 using SPAdes.

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