This website collects some notes, tutorials and handsout used for microbial bioinformatics training events.

Building a pipeline with Nextflow DSL2

Programme page

• A de novo assembly pipeline: we will design a simple workflow to assemble and annotate microbial genomes
• Gathering the tools: we will use Miniconda to gather our required tools, and generate Docker and Singularity containers manually (Nextflow can automate this step, but it’s good to practice manually first)
• First steps with Nextflow: we will install Nextflow and run a couple of test scripts
• The de novo pipeline in Nextflow: we will implement our pipeline in Nextflow

Metabarcoding workshop

• Day1 - Introduction, Qiime2 and QC
• Day2 - From the feature table to diversity analyses
• Day3 - Analyse your data in R

Metabarcoding Workshop Programme

Metagenomics workshop: classifying your reads

• Day1 - Introduction and preliminary aspects
• Day2 - Kraken2, Bracken, Krona and MultiQC
• Day3 - Analyse your data in R

Kraken2 Workshop Programme

Introduction to the Bash scripting

You learnt how to work from the command line, and now want to start automating your actions with scripts. This is a gentle introduction for you.

• Introduction and first examples
• For loops
• if conditionals
• Safety net
• Getting parameters