- Course overview
- Search within this course
- Introduction
- Course materials and software
- Metagenomics bioinformatics – course introduction
- Quality control and host decontamination
- The European Nucleotide Archive
- Tools to assemble short reads
- MGnify services
- MGnifyR
- Binning and MAG generation
- ENA metagenomics standards
- MGnify MAG resources
- Strain resolution
- Tools for comparative metagenomics
- Your feedback
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Quality control and host decontamination
Varsha Kale, a bioinformatician in the Microbiome Informatics team, explains the concepts of quality control (QC) for microbiome sequencing data.
This talk explores the reasons for carrying out QC on sequence data before downstream analysis, and some potential sources of contamination that are useful to consider in designing a study. The following broad aspects of QC are covered:
- General statistics
- Read trimming
- Removal of sequence artifacts
- Host decontamination
DOWNLOAD PDF SLIDES
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Practical
You can practice the process for QC filtering, the different steps applied when filtering sequencing data prior to analysis, and understand the QC display by following this practical tutorial. It includes exercises with which you can explore and apply the MGnify QC filtering steps on an example dataset.
All the necessary information you need for this practical can be found below:
- Practical guide:
- Docker container: