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DPL-193 Scoping for Open Sourcing PSD applications #168

Closed stevieing closed 2 years ago

stevieing commented 2 years ago

Description Scoping for Open Sourcing PSD applications:

Who the primary contacts are for this work Steve

Knowledge or Stake holders Other people that may have specific knowledge about this work or have a stake in how it is implemented. e.g. John Smith is an expert on x

Additional context or information Any other useful context or information that may be useful.

stevieing commented 2 years ago

Notes from Genomics England meeting:

Receive samples fluidx Scan rack DNA only all fridge based Manifest manual check IDs already in gel database with metadata Rename tubes 10 digits Manually creating codes Internal sample Id

Generating barcodes and writing them on

Row for each sample and adding metadata

Qc output manually entered.

Now Receive random tube that is not trackable.

Needs to be reracked.

Sequencing Promethion Experiment name id Position Id Flow cell id Sample id

Shearing Sre Beads Library prep Femto Femto output Manual calculations

dataTable_headers.xlsx GEL Lab Processing Overview.pptx template_sampleSheetImport_PROM1.csv

stevieing commented 2 years ago

Notes from Genomics England informatics meeting:

When a sample comes into the lab scan barcode and find out whether it already exists.

Identifiers to pull out of clinical system to use in the LIMS.

How to process the sample.

qc outputs. femto pulse ??

produce sample sheets.

Qc output from pipelines into LIMS.

Original sample manifest. Hopefully as standard that sample will be registered in the Genomics England clinical database. Assign a barcode to each sample in a tube. Lab person would scan the barcode into LIMS and LIMS would make a call to GE database which would retrieve any information that they need. qc done on original sample which would determine what they do next e.g may need to shear it. Create libraries and go into a new tube with a new barcode. Make a decision on which libraries go on which flowcells ( 2 flowcells for cancer samples and 1 for normal samples ). Generate a sample sheet which you would upload to the Promethion. Generate run names and ids - lab sample id. Related to filenames.

Advanced: uploading qc data using the ONT API.

stevieing commented 2 years ago

What would we need to do to make traction open source ready (1/03)?

KatyTaylor commented 2 years ago

Closing, as is in Done column.