Week beginning November 24th 2025
Andrea Telatin and Alise Ponsero, QIB Core Bioinformatics
This module has a dedicated website
that we will use to store training materials and hands-on tutorials
Monday 24th, UG55C
Morning
- Microbiome genomics: profiling vs de novo
- Tools: Kraken2, Bracken, Biobakery, Kaiju, …
- Practical: MetaPhlAn / HUMAnN
Afternoon
- Sequence Coverage and assembly
- Tools: MegaHit, Minimap2, Samtools, BamToCov, CoverM
- Practical: De novo assembly and read recruitment
Tuesday 25th, UG55C
Morning
- Quality checks: assessing sequencing quality (adaptors, etc), library quality (negative controls) and sample quality (host contamination)
- Tools: FastQC, fastp, fastqlong, seqfu, kraken2, hostile
- Practical: Host removal using Hostile
Afternoon
- Binning contigs
- Practical: SemiBin2
Thursday 27th, UG44B
To be defined
This day we will focus on exploring datasets using Anvi’o or using command line tools to perform strain tracking and k-mer sketches. This is subject to technical details that will be assessed before the training.
Friday 29th, UG55C
Morning
- Functional characterization
- Tools: HUMAnN, Metaprokka, CoverM, …
- Practical: extracting metabolic pathways of interest