Microbiome and Metagenome Data analysis workshop, June 4-8, 2018

[richard.nadvornik]

Ceske Budejovice, Czech Republic, See here for full event details and apply online

This workshop covers microbiomics / metagenomics analysis from quality control, filtering and assembly/clustering to taxonomic classification, functional assignment and comparative metagenomics.
Both community analysis of amplicon sequencing data as well as analysis of whole genome shotgun sequencing data will be covered including methods for statistical comparisons of multiple metagenomic samples.
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 life scientists and bioinformaticians working or being interested in the field of metagenomics / microbiomics. No prior knowledge of metagenomic / microbiomics sequences 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 - Get to know the environment

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

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

• Current NGS technologies
• Quality control of sequence data
• Editing sequences in various programs
• Introduction to alignment

Day 3: Read mapping and alignment visualization - The must-have skills

• Read mapping
• Quality control of alignment sequencing data
• Alignment visualization

Day 4: Metataxonomic analysis - The Amplicon Session

• Amplicon sequencing of marker genes
• Analysis of marker genes - practical part
• Data preparation (sequence trimming, quality filtering, OTU clustering)
• OTU table construction and OTUs classification
• Evaluation of results from metataxonomic analysis

Day 5: Metagenomic analysis - The Shotgun Session

• Metagenome data processing and de novo assembly
• Analysis of metagenomics data - practical part
• Data preparation (adaptor trimming, quality filtering, digital normalization)
• Annotation of contigs (MG-RAST)
• Mapping reads to contigs (gene coverage/quantification, sample comparison)
• Binning (MaxBin2)
• Evaluation of results from metagenomic analysis

See here for full event details and apply online