DeNovo Assembly and Variant Calling Data Analysis Workshop, Oct 8-12, 2018, Prague

[richard.nadvornik]

4th Prague Autumn School, Prague, Czech Republic, See here for full event details and apply online

After three successful years we are again inviting you to join our data analysis workshop which covers all basic steps of Next-Generation sequencing data analysis.
This five day computationally-intensive workshop focuses on quality control, sequence editing, read mapping and alignment. Additionally, this year we will pay a special attention to genome assembly and variant calling and annotation.
You will be briefly introduced into the Linux operating system and in this environment you will analyze sequencing data using various publicly available tools.

Who should attend?
This workshop is aimed at beginners as well as advanced users, life scientists and bioinformaticians interested in the analysis of Next-Generation sequencing data. No prior knowledge of sequences data analysis or specific programming skills are required.

During the workshop…

• Trainers will provide lectures with follow-up hands-on exercises in order to have the participants learning and assessing their knowledge
• All workshop participants will perform all steps of data analysis tasks themselves!
• The powerful computer infrastructure available at the conference center will be used (no personal laptops are required/allowed)

Workshop agenda:
Day 1: Linux as a scientific tool - Go beyond the graphical user interface!

• General introduction to data analysis
• Unix environment for bioinformatic analysis
• Introduction to the Linux system
• Basic commands in Terminal and their practical use
• Overview of common data formats

Day 2-3: Basic operations with NGS data - Get a full picture of NGS workflow!

• Working with data from NCBI and other databases (SRAtool kit)
• Quality control of sequence data (FastQC, MultiQC, …)
• Editing sequences in various programs (FASTX-Toolkit, …)
• Introduction to alignment
• Read mapping (BWA, Bowtie2, …)
• Preparation of the reference sequence
• Alignment visualization (Tablet, IGV, UCSC, …)

Day 4: De novo assembly - Theory and hands on until you master...

• Different approaches to de novo assembly (Velvet, SPAdes, …)
• Evaluating assembly (Quast, …)
• Assembly visualization (Tablet, …)

Day 5: Variant Calling - Explore the open source world of variants

• Preparation of sequencing data
• Identification of variants - SNPs, INDELs (SAMtools, GATK, …)
• SNP analysis
• Annotation of variants (SnpEff)
• Visualization of variants

See here for full event details and apply online