Overview of WGS Library Prep and Sequencing Options

OPTION 1

There are three basic options for generating whole genome resequencing libraries.

  1. Extract DNA and generate your own libraries

  2. UC core facility extracts DNA and/or generates libraries for you

  3. CCGP Mini-Core extracts DNA and/or generates libraries for you

Option 1. PI-generated libraries

Extract DNA and generate your own libraries. Most PIs have indicated that they will extract gDNA and generate their own libraries.

  1. Library prep method: Library preparation method is up to individual labs to choose so that these data will fit in with your preferred workflows and be compatible with your non-CCGP projects.

  2. Indexing: We strongly recommend dual indexing to avoid index hopping. See this site for more information.

    There are two index options:

    A. Preferred. Use indexes provided by UC Berkeley

    1. CCGP projects may submit partial lanes to UCB

    2. UCB will pool with other compatible libraries to maximize lane efficiency and minimize sequencing cost per sample

    3. Sequencing will be billed as a percentage of the lane used

    4. Email gsl-fgl@berkeley.edu to request index plates from UCB (please include shipping address)

    5. To submit these samples for sequencing:

      a) Follow the standard llumina Novaseq submission protocols from UCB: https://qb3.berkeley.edu/facility/genomics/

      b) Complete this coordinating spreadsheet and email facility manager Carrianne Miller with a 2-week notice

      c) Note in the submission that the submission contains CCGP samples

      d) Include the index plate/well information for each sample

    B. Use your own indexes

    1. Core sequencing facilities generally will not pool your samples with other projects if you use your own indexes because they cannot guarantee that indexes from different projects are compatible

    2. You can maximize lane efficiency (and cost) if you completely fill out a lane

    3. You may sequence at any UC sequencing core

  3. Pooling: Keep in mind that in most cases, cores will charge a per sample fee for pooling libraries into a sequencing pool. Please contact the core to confirm pricing and logistics.

    • If you do choose to have the core pool your libraries, submit individual samples in tubes only (DO NOT submit samples in plates)