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  • hetappi
    Junior Member
    • Feb 2011
    • 8
    #1

    Combining PacBio assembly with 10X assembly?

    Dear all,
    Currently we created an assembly of a highly repetitive plant genome with
    60x coverage of Pacbio reads (assembler HGAP4).

    In addition we have 100x coverage with 10X Illumina reads. These were
    assembled using the supernova assembler.

    Has anyone ideas how we could combine these two assemblies? The genome
    size is about 2Gbases.

    any help appreciated

    hetappi
    Tags: 10x genomics, assembly, hybrid assembly, pacific biosciences
    • hetappi
      Junior Member
      • Feb 2011
      • 8
      #2
      Now I used the program scaffold_builder, see
      Scaffold_Builder
      https://sourceforge.net/projects/scaffold-b/
      Download Scaffold_Builder for free. Combining de novo and reference-guided assembly with Scaffold_builder. Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N's and small overlaps are aligned with Needleman–Wunsch algorithm and the consensus created with IUPAC codes.


      This program did run for a few days and then it produced
      a SINGLE CONTIG of 2GigaBases. I am a little bit in doubt about
      this fabulous result.

        Comment

        • horvathdp
          Member
          • Dec 2011
          • 66
          #3
          Hi, did you eventually come to a good conclusion with your study? I have a similar situation, and would love to know what worked for you.

            Comment

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