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NGS Data Analysis and Workflow Management

Overview

Requirements

Content

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What will you learn?

In this online training, you will learn the most important aspects of NGS data analysis. In addition to handling large NGS datasets and data formats, the focus is on creating complete DNA workflows in Galaxy and Snakemake/Nextflow. Starting with quality control and moving to variant calling, you will first learn how to create DNA workflows in Galaxy and then transfer these steps to the script-based open-source workflow management systems Snakemake/Nextflow. With Snakemake/Nextflow, you can create bioinformatics pipelines independently and reproducibly, allowing for the automatic execution of all necessary analysis steps.

What will you achieve?

Upon completing the training, you will have learned the following:

Detailed understanding of NGS file formats (FASTQ, SAM/BAM, VCF).
Processing large NGS datasets.
Navigating the file system using simple Bash commands via the command line.
Introduction to the software manager Conda.
Using the command line to apply analytical software.
Applying open-source software for all analytical steps.
Creating a complete DNA analysis workflow in Galaxy (from quality control to variant calling).
Transferring this knowledge to create reproducible and scalable workflows in Snakemake/Nextflow.

Certificate: Upon successful completion of the training, you will receive a certificate from CQ Beratung+Bildung GmbH.

What funding opportunities are available?

CQ is AZAV-certified as a training provider and the ‘Bioinformatics and Biostatistics’ training course is approved for employment promotion. The subject of NGS is part of the certified course and can be subsidised with an education voucher.

Please note the following important information for the Employment Agency/Job Center: Measure No. 962/26/2024.
Contact your Employment Agency about the subsidised further training course for occupational health assistants. You are welcome to use our information sheet.

Alternative funding options for further trainings and coachings can be found here.

Useful tips

This course is taught exclusively in English. We will be happy to advise you on your participation options.

Use our free SCS short web seminar to familiarize yourself with Single Cell Sequencing.
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Who is the training aimed at?

The target group includes academics in biology, microbiology, chemistry, biochemistry, medicine, mathematics and phaysics.

Your qualification

Professionally:

Basic knowledge of molecular biology, especially genetics/genomics.
Fundamental understanding of molecular/sequencing technologies (PCR, DNA libraries, Illumina sequencing).
Experience in Linux/Bash, R and/or Python is required.

Technically:

A computer with at least 30 GB of free disk space.
Operating system: Windows, Linux (Ubuntu/Virtual Machine), or Mac OSX.
A current browser (Firefox or Chrome).
Stable internet connection, camera, speakers, and a microphone. Ideally, we also recommend having two screens, or at least one larger screen.

Your motivation

Efficient and high-quality data analysis of genomic information (DNA) is becoming increasingly important for answering biological and medical questions. This is made possible by the latest Next-Generation Sequencing technologies, which is why bioinformatics skills in handling very large datasets are increasingly in demand.

Topics and procedure

Modul 1: Analysis of NGS Data

Introduction to NGS data (Illumina, single- and paired-end data, Phred quality scores)
Familiarization with NGS data formats (FASTQ, SAM/BAM, VCF)
Processing sequencing data (quality control, trimming, mapping)
Creating a variant call workflow in Galaxy and Snakemake/Nextflow
Visualization of NGS data with Integrated Genomic Viewer (IGV)

Modul 2: Introduction to Command-Line Tools and Software Management

Using Conda to create and manage software environments for NGS data analysis
Installation and application of command-line tools (e.g., samtools, Trimmomatic)

Modul 3: Introduction to Workflow Management Systems

Basic principles of NGS workflows with Galaxy (browser-based)
Creating NGS workflows in Snakemake/Nextflow (script-based, command line, basics of bash)

Technical requirements

A computer with at least 30 GB of free hard disk space.
Operating system: Windows, Linux (Ubuntu/Virtual Machine), or Mac OSX.
A current browser (Firefox or Chrome).
Stable internet connection, camera, speakers, and a microphone. Ideally, we also recommend having two screens, or at least one larger screen.