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-   -   Shotgun metagenomics study for environmental samples using PacBio (http://seqanswers.com/forums/showthread.php?t=78177)

weigrc 09-20-2017 01:20 AM

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 :confused:

Markiyan 09-20-2017 05:08 AM

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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