Shotgun metagenomics study for environmental samples using PacBio

[weigrc]

Dear all,

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


Thanks,
Wei

[Markiyan]

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.