e-learning
Removal of human reads from SARS-CoV-2 sequencing data
Abstract
Patient samples for pathogen detection are usually "contaminated" with human host DNA.
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 can you remove traces of human sequence data from a sequenced viral sample?
Learning Objectives
- Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources
- Organize the data into a collection
- Preprocess and map the data against the human reference genome
- Eliminate reads/read pairs that map to the human genome from the original data
Licence: Creative Commons Attribution 4.0 International
Keywords: Sequence analysis, covid19
Target audience: Students
Resource type: e-learning
Version: 5
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- Mapping
- Quality Control
- Using dataset collections
Learning objectives:
- Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources
- Organize the data into a collection
- Preprocess and map the data against the human reference genome
- Eliminate reads/read pairs that map to the human genome from the original data
Date modified: 2023-11-09
Date published: 2021-08-04
Scientific topics: Sequence analysis
External resources:
Activity log
