Hands-on bioinformatics for microbial meta-omics
ENV-621 / 3 credits
Teacher(s): Altshuler Ianina, Bell Emma, Bernier-Latmani Rizlan, Carratala Ripolles Anna
Language: English
Remark: You will need to install software on your laptop to be able to participate in this course. The second half of the course will take place February 5-9, 2024.
Frequency
Every 3 years
Summary
This course will train doctoral students to use bioinformatic tools to analyse amplicon and metagenomic sequences. In addition, we will also touch upon meta-transcriptomics and meta-proteomics.
Content
Theory:
Introduction to Omics and DNA sequencing technologies
DNA sequencing and uncultured microorganisms
Reproducible research and community standards
Metagenome sequence assembly overview
Intro to read mapping and mapping tools
Reconstructing genomes from metagenomes
Intro to Annotation, databases, HMMs
Practical:
Intro to command line / computing resources
QC reads, Adaptor Removal
Assembly
Assembly stats
Gene prediction
Mapping
Binning
Bin refinement
Bin QC
Dereplication
Abundance
GTDB
Phylogenomics
Functional Annotation
Note
Dr. Emma Bell
In the programs
- Number of places: 20
- Exam form: Oral presentation (session free)
- Subject examined: Hands-on bioinformatics for microbial meta-omics
- Lecture: 40 Hour(s)
- Practical work: 40 Hour(s)