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  • Hybrid assembly of PacBio and Illumina

    I would like to know how people are handling hybrid assemblies of PacBio and Illumina. Are Velvet or the CLC-Bio good choices?

    Thanks for your input
    AlLo

  • #2
    I know Bastien has been working on PacBio support in MIRA, which already supports Roche 454, Solexa/Illumina and Sanger reads for hybrid assemblies.

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    • #3
      ALLPATHS-LG has support for Illumina / Pacbio combined assemblies, but I understand it has quite strict requirements as to the particular type of input you give it. Nevertheless, check it out.

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      • #4
        There is a plug-in of the latest Celera assembler, PacBioToCA, written by Sergey Koren at NBACC, that uses illumina reads to error-correct PacBio reads and outputs a frg file for OLC assembly in the CA. We have used this to great success for bacterial genomes (with assistance from Sergey and Adam Phillippy). I think that Bastien's approach has been more one-step, i.e. incorporating the reads directly into the assembly, but I haven't attempted to compare the results. The v1.3 software from PacBio purports to support hybrid assembly as well, with claim to be better than the CA approach, but I haven't tried very hard to make it work or compare it rigorously since we already had the other pipeline working before v1.3 was released.

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