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  • re-implement
  • sample submission change requests
  • suggest implementing as part of LSCLC Cores LIMS
    • Single Sign-in with other cores. consistent customer interface for all services.
  • could populate information in Minilims module, or customer development within LSCLC LIMS
  • Can probably use the order forms in minilims
    • Billing probably ultimately still goes through LSCLC LIMS - perhaps we should talk with Brianne because low volume billing might be doable with minlims capability and some low impact manual process by the office staff (unlike the high volume LSCLC invoicing). It keeps GBS separate completely from LSCLC (not sure if that is good bad or indifference)
    • if not using LSCLC for billing, not so strong of a need to tie authentication/authorization from minilims to LSCLC LIMS.
    • if not using LSCLC, credit card processing NOT possible
  • Sample submissions are required to be in a plate format with 95 samples and 1 random blank. 
  • We ask for concentration, but we re-quantify and it would be great to be able to enter those new numbers into the database.

Integration with Sequencing Submission

  • Currently I have to enter sample information onto the Core Facility website by hand.  Automation of this would be complicated by my need to assign billing to different accounts.  In addition, after Tom has made the flowcell I go onto Wikilims to get the flowcell name and lane assignments for the samples I submitted. 
  • If samples are going to be sequenced off site then, in addition to the above steps I need to create additional emails and packing slips.

QC Scripts

  • QC Scripts
  • Comments and request changes for QC output
  • Besides the changes I listed above, but the biggest bug is that the scripts look for the cut site overhang and then the barcode.  Barcodes containing the cut-site overhang are not recognized and we see it as 0 reads.  The data pipeline does barcode and cut-site recognition simultaneously and so you still get data for these barcodes.
  • It would be great to get some reports off of the Illumina machine.

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