e-learning
Calling variants in non-diploid systems
Abstract
The majority of life on Earth is non-diploid and represented by prokaryotes, viruses, and their derivatives, such as our own mitochondria or plant's chloroplasts. In non-diploid systems, allele frequencies can range anywhere between 0 and 100% and there could be multiple (not just two) alleles per locus. The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bacterial genomes,.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How does frequency of mitochondrial polymorphisms change from mother to child?
Learning Objectives
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.
Licence: Creative Commons Attribution 4.0 International
Keywords: Variant Analysis, microgalaxy, prokaryote
Target audience: Students
Resource type: e-learning
Version: 23
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- Mapping
- Quality Control
Learning objectives:
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.
Date modified: 2024-03-15
Date published: 2017-02-16
Contributors: Alex Ostrovsky, Anton Nekrutenko
Scientific topics: Genetic variation, Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis
Activity log
