Implement DNA Workflow chain for RNA Lab

[tim-snyder-wustl]

Note: This task is too large for one ticket. Break this ticket up in to smaller tickets.

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Clone the current RNA NGS workflow chain (via YML file) for Toni's lab and adjust accordingly for handling DNA.

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Entities to add

• DNA (same fields as RNA) with new suffix for GTAC ID = 'D'

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Workflows to add

• Capture
  • identify fields for new kits (TBD)
  • could send libraries or pooled libraries to Capture wf. Samples would be routed back to a library QC step. Could then sumbit to recieve library or library pooling (could also pool the pools)
  • this is a sub protocol of whole genome - create a whole genome library, take a subset and run it through this protocol.
    • can be run as pool
    • single samples, then pool for sequencing
    • re-qc the aliquot from the capture and go to pooling or straight to sequencing

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Workflows to modify

There are no intermediates for the DNA workflow chain! Will need to remove them once the RNA workflow chain has been cloned.

• Accessioning
  • add kit types:
    • Whole Genome
    • Capture Agilent Human CRE
    • Capture Agilent Mouse
      • Capture Agilent Custom
    • ChIP
    • Amplicon
• RNA (DNA) Extraction
  • add kits (TBD, leave what is there now for RNA, will need to get from Chris eventually)
• RNA (DNA) Library Prep
• RNA (DNA) QC Bioanalyzer
  • add assays: -DNA 1000 (12/chip)
    • High Sens. (11/chip)
• RNA (DNA) Tapestation
  • add assays:
    • gDNA
    • D1000
    • HS D5000

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Workflow Chain Diagram

[tim-snyder-wustl]

From Toni regarding custom transition strategies for the workflow chain (we do not need any):

For DNA preps, we are not creating intermediates (cDNA, mRNA) like we do for RNA pipeline, so I don’t think we will need to do that. Unless you want to treat the exome libraries like that (create a “prehyb” intermediate library, rather than having to transition to another workflow for the posthyb steps). To me, it makes more sense to do it as another workflow step than as an intermediate, because in some cases we may sequence both the intermediate library and the exome library (*which might be tricky as well).

exome library == illumina library