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Shotgun metagenomics study for environmental samples using PacBio

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  • Shotgun metagenomics study for environmental samples using PacBio

    Dear all,

    Anyone has such experience? How to conquer the issue of low input DNA?


    Thanks,
    Wei

  • #2
    Make sure to have Illumina data from the same DNA prep for efficient error-correction

    Two points:

    1. To get more DNA try making the sample prep more efficient/use more starting material/

    2. To allow efficient error-correction of the pacbio reads also prep PCR-free (optional: + Nextera matepair) libraries from the same lot of DNA as used for creating the PAC-Bio libraries, and sequence them at 30X coverage compared to the volume of the raw pacbio data you are getting.

    First do self-errorcorection of the pacbio subreads from the same template,
    than error correct the filtered pacbio subreads using the Illumina data before the assembly.

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