Competency information
Details
Perform quality control, data validation (on eukaryotic and prokaryotic data) using open-source and or commercial tools.
Considerations
- Quality metrics for NGS data.
- Open source and commercial NGS tools.
- Ethical and governance frameworks.
Next Generation Sequencing platforms
- The genome science behind NGS – random fragments, sequencing, assembly.
- Different sequencing platforms and the physical technologies they deploy, including semiconductor, optical, nanopore.
- Applications of NGS.
Sequence assembly
- The problems of aligning short reads.
- Next generation alignment strategies, e.g. Bowtie, Short Oligonucleotide Analysis Package (SOAP), Burrows-Wheeler Alignment (BWA), de Bruijn graphs.
- Data formats for next generation data, e.g. BAM, SAM, fastq.
- Sequence interpretation.
- SNP detection, CNV detection.
- Oral and written communication skills.
Relevant learning outcomes
# | Outcome |
---|---|
# 2 | Outcome Analyse NGS data through base calling, filtering, quality control, data validation and read mapping (eukaryotic and prokaryotic) in a clinical setting.(The clinical setting could include Clinical Genetics, Microbiology, Virology, Clinical Diagnostics, for example targeted oncology treatments/classical genetics.) |