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Title: "Bioinformatics for Metagenomics in the Diagnostic Laboratory- Linux & Flowcraft" \
Author: "C I Mendes" \
Date: "October, 2018" 
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Overview

This practical session will introduce state-of-the art analysis of Illumina paired-end shotgun metagenomic data in the context of the Diagnostic Laboratory. Participants will learn the basis of interaction with Linux Operating System with Shell commands through a terminal windows, and how to use the Flowcraft tool to build and execute pipelines to asses microbial composition, resistance gene detection and typing.

Target audience

Participants of ESCMID's capacity-building workshop for Metagenomics in the Diagnostic Laboratory

Learning objectives

• Basic Concepts of Linux and Shell Commands

• Basic Concepts of Nextflow and Software Containerization

• Overview of FlowCraft

• Building a Pipeline with FlowCraft - Recipes and Build Mode

• Running a Pipeline - Inspector Mode

• Obtaining Interactive Reports

Plannification

1. Linux Fundamentals

1.1 What is the Shell and Why do you need it?

1.2 First Commands

1.3 What Else is Out There

1.4 Useful Material

2. Nextflow and Software Containers

2.1 Reproducibility of a Program

2.2 Software Containers

2.3 The Nextflow

3. FlowCraft

3.1 Overview

3.2 Installation and Dependencies

3.3 Building a pipeline

3.3.1 The build mode

3.3.2 Recipes

3.4 Running a Pipeline

3.4.1 The Inspector mode

3.5 Obtaining a Report