Inhaltspezifische Aktionen

Genomics training course 21.-23.09.2016

Agenda Genomics training course 21.-23.09.2016

 

The first day will introduce the ReadXplorer software for the the analysis of short read mapping data:

  • Handling of complex experimental settings in the ReadXplorer user interface
  • Automatic analysis of re-sequencing experiments (SNP detection, coverage statistics, ...)
  • Automatic interpretation of RNA-Seq experiments (differential gene expression, transcription start site detection, operon analyses, …)


The second day will give a comprehensive introduction into microbial genome annotation. Available tools and algorithms for the different assembly and annotation steps will be explained. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline:

  • The basics of genome assembly
  • The basic principles of regional and functional annotation
  • Genome annotation pipelines
  • Manual and distributed genome annotation using GenDB


The third day will give an introduction into comparative genomics with a focus on differential gene content analysis using the EDGAR platform.  The use of the BLAST score ratio values (SRVs) to measure the similarity between coding sequences and to assess orthology will be introduced. All features of EDGAR will be introduced in detail:

  • Genomic subset calculations (core-genome, pan-genome, singleton genes)
  • Core-genome-based phylogenetic analyses
  • Sequence based phylogeny
  • ANI, AAI, GGDC
  • Statistical analyses (core/pan/singleton development plots)
  • The public EDGAR database


On all three days the program includes extensive hands-on training to allow participants to get familiar with the presented software. Participants can bring own datasets that fit the topics of the workshop. The data can be analyzed in the hands-on sessions.


We have to demand a 30 Euro fee to cover our expenses for catering, apart from that the workshop is free.


Contact: Gwyneth.Schulz@computational.bio.uni-giessen.de




Day 1: ReadXplorer

  • 11.00 13.00: Transfer of datasets
  • 13.00 – 15.00: ReadXplorer
  • 15.00 – 15.30: Coffee Break
  • 15.30 – 17.00: ReadXplorer hands-on

Day 2: Microbial Genome Annotation

  •   9.00 – 10.30: Assembly
  • 10.30 – 11.00: Coffee Break
  • 11.00 – 12.30: Annotation
  • 12.30 – 13.30: Lunch
  • 13.30 – 14.30: ASA3P
  • 14.30 – 15.00: Coffee Break
  • 15.00 – 17.00: GenDB hands-on

Day 3: Comparative Genomics

  •   9.00 – 10.30: EDGAR
  • 10.30 – 11.00: Coffee Break
  • 11.00 – 12.00: EDGAR hands-on
  • 12.00 – 12.30: Closing Remarks
  • At the afternoon of Day 3 participants can discuss open questions or personal projects/data with the course experts.




Funding:

The de.NBI project is funded by the BMBF.
FKZ 031A532 — 031A540