De Novo Genome Assembly Using Next-Generation Sequence Data
Aligning and Merging Fragments of DNA
When?
8 - 10 February 2016
Where?
iad Pc-Pool, Rosa-Luxemburg-Straße 23, Leipzig, Germany
Link?
http://www.ecseq.com/workshops/workshop_2016-02-De-novo-genome-assembly
Scope and Topics
This workshop focuses on the genome assembly of non-model organisms. While analyses of model organisms generally rely on a reference genome, studies of non-model organisms usually lack this advantage. Thus, the de novo assembly of a non-model organism poses some unique challenges.
The first workshop module is an introduction to NGS data analysis using Linux, assuring that all participants are able to follow the practical parts. The most important NGS file formats (fasta, fastq etc.) are introduced and are followed by first hands-on analyses (quality control (QC), visualization etc.). You will learn how to read and interpret QC plots, clip adapter sequences and/or trim bad quality read ends. In the second module de novo assembly methods are introduced. Different techniques are explained and compared and you will learn how they differ from reference-based assemblies. You will perform your first de novo assembly. In the last module you will learn how to judge the quality of a de novo assembly and how the results of different assembly approaches can be compared.
Workshop Structure
- NGS for beginners: This module will introduce the essential tools and file formats required for NGS data analysis. It helps to overcome the first hurdles when entering the field of de novogenome assemblies. Different methods of NGS will be explained, the most important notations be given and first analyses be performed.
- Introduction to de novo genome assemblies: This day covers essential knowledge for the understanding what de novo assemblies are and how they differ from reference based assemblies. You will learn how you can estimate the size of your target genome and perform your first assembly.
- Understanding de novo genome assembly results: You will learn how to assess the quality of a genome assembly. You will then apply this knowledge to the result of your first assembly.
Requirements
- Basic understanding of molecular biology
- For the Introduction to NGS Data Analysis and downstream courses: basic linux & bioinformatics knowledge (shell usage, common commands and tools). You should be familiar with the commands covered in the Learning the Shell Tutorial
Target Audience
- Biologists or data analysts with no or little experience in NGS data analysis
Included in the Course
- Course materials
- Catering
- Conference Dinner
Key Dates
- Opening Date of Registration: 1 October 2015
- Closing Date of Registration: 15 January 2016
- Workshop: 8 - 10 February 2016 (8 am - 5 pm)
Attendance
- Location: iad Pc-Pool, Rosa-Luxemburg-Straße 23, Leipzig, Germany
- Language: English
- Available seats: 24 (first-come, first-served)
Registration fees
- registration fee: 998 EUR (without VAT)
Travel expenses and accommodation are not covered by the registration fee.
Contact
ecSeq GmbH
Brandvorwerkstr.43
04275 Leipzig
Germany
Email: events@ecseq.com
Register here
