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Old 09-20-2017, 12:20 AM   #1
weigrc
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Location: Hong Kong

Join Date: Oct 2011
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Default 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
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Old 09-20-2017, 04:08 AM   #2
Markiyan
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Location: Cambridge

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Lightbulb 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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