GBS Project

Overview

This is a project to replace and enhance existing laboratory management systems supporting the Institute for Genomic Diversity's Genotyping By Sequencing (GBS) service.

IGD Please add overview description

Workflow

I'm thinking of a fairly high level text list of steps from project initiation to data distribution and billing - general terms like "run QC scripts" or "customer places online order"

1. Project Initiation
   • Requires personal contact with lab director
2. xxx
3. xxx
4. Raw Data -> Data Files
   • Pipeline can be Tassel, or Fei Li's pipeline
5. Data Interpretation
   • "manual" / "art"
6. Data Distribution

Current Components

Overview

GBS Database Schema

sample submission interface fields and database schema

QC Scripts

"SampTrack" C# windows program to interface with GBS for setting up pools etc.

manual SQL queries (supplement "samptrack")

redmine project management

• Project initiation
  • create project in redmine

    Data Distribution

• how accomplished now?

  billing

  Misc operations

• Configure new adapter plate configurations
  • example adapter plate spreadsheet

Map current components/workflow to new system(s)

Misc operations

• Configure new adapter plate configurations
  • self service interface/upload?