Genetic data production

[sylvainschmitt]

Symphonia geonmics

• [x] Choose kit
• [x] Select target sequence to be captured
• [x] Design probes (target sequences to be sent to the company)
• [x] Extract DNA
• [x] Prepare libraries
  • [x] Normalisation
  • [x] Digestion
  • [x] Adaptor ligation
  • [x] Size selection (1 col remaining)
  • [x] Tagging and amplification
  • [x] Amplification check
  • [x] Library repeat
  • [x] Capture
• [x] Sequencing
  • [x] Quantify DNA
  • [x] Build equimolar pools for lanes
• [ ] Raw data analysis
  • [x] Quality check
  • [x] Trimming
  • [x] Targets mapping
  • [x] Reference mapping
  • [ ] de novo assembly
  • [ ] de novo reference mapping
  • [ ] Genome by Sequencing (GbS)
  • [ ] SNP call
  • [ ] SNP filtering

Eschweilera geonmics

• [x] Sampling
• [x] Select target sequence to be captured
  • [x] Functional targets (Oscar transcripts)
  • [x] Neutral targets (ddRAD consensus sequences)
• [x] Design probes (target sequences to be sent to the company)
• [x] Extract DNA
• [ ] Prepare libraries
  • [x] Purification
  • [x] Dosage (NanoDrop adjusted Qubit)
  • [x] Concentration (SpeedVac)
  • [x] Normalization
  • [x] Library test (2 samples)
  • [ ] Digestion (1')
  • [ ] Adaptor ligation
  • [ ] Tagging and amplification
  • [ ] Purification
  • [ ] Dosage (PicoGreen)
  • [ ] Equimolar pools preparation
  • [ ] Pools fragment size evaluation (Bioanalyzer)
  • [ ] Pools fragment size selection (Pippin)
  • [ ] Capture
• [ ] Sequencing
  • [ ] Quantify DNA (Qubit/qPCR)
  • [ ] Equimolar pools for lanes
• [ ] Raw data analysis
  • [ ] Quality check
  • [ ] Trimming
  • [ ] Targets mapping
  • [ ] Reference mapping
  • [ ] de novo assembly
  • [ ] de novo reference mapping
  • [ ] Genome by Sequencing (GbS)
  • [ ] SNP call
  • [ ] SNP filtering

[sylvainschmitt]

Issue split in two new issues