Organizer: de.NBI

Start: Monday, 04 May 2020 @ 09:00

End: Wednesday, 06 May 2020 @ 17:00

Venue: Gießen

City: Gießen

County: Gießen

Country: Germany

Description:

Educators:
Alexander Goesmann, Sven Griep, Oliver Rupp, Tobias Zimmermann, Oliver Schwengers, Andreas Hoek, Jochen Blom, Sebastian Jaenicke (BiGi)

Date:
04.-06.05.2020

Location:
Heinrich-Buff-Ring 58, Justus-Liebig-Universität, Gießen, Seminar Rm. 0024a

Content:
The first day will introduce software tools for the quality control of short read data. For conducting basic sequence read processing steps we will use our local Galaxy server. In the last session we will explain the basic approaches for genome assembly and run various genome assemblers:

  • Introduction to quality control
  • Automatic trimming of sequencing reads
  • The basics of genome assembly

On the second day we will take a closer look at the genome assembly results. Afterwards, we provide a comprehensive introduction to microbial genome annotation. Available tools and algorithms for the different genome analysis and annotation steps will be explained and used within Galaxy. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline (ASA3P) that can be used to process thousands of genomes on a single day:

  • The basic principles of region and function annotation
  • Genome annotation tools and pipelines in Galaxy
  • Manual and distributed genome annotation using GenDB
  • Introduction to the ASA3P software

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
  • Statistical analyses (core/pan/singleton development plots)
  • The public EDGAR database

Agenda:

Day 1: Quality control & genome assembly

13:00 – 13:15 Welcome & introduction (Alexander Goesmann)
13:15 – 13:30 Transfer of data sets
13:30 – 15:00 Read quality control & trimming incl. hands-on session (Sven Griep, Oliver Rupp)
15:00 – 15:30 Coffee Break
15:30 – 17:00 Introduction to genome assembly incl. hands-on session (Sven Griep, Oliver Rupp)

Day 2: Microbial Genome Annotation

9:00 – 10:30 Introduction to microbial genome annotation (Alexander Goesmann)
10:30 – 11:00 Coffee Break
11:00 – 12:30 Genome annotation with Galaxy & GenDB hands-on session (Sven Griep, Oliver Rupp, Tobias Zimmermann)
12:30 – 13:30 Lunch
13:30 – 14:30 Introduction to ASA3P (Oliver Schwengers)
14:30 – 15:00 Coffee Break
15:00 – 17:00 ASA3P practical session (Oliver Schwengers, Andreas Hoek)
17:30 Optional: Tour to Gleiberg castle

Day 3: Comparative Genomics

9:00 – 10:30 EDGAR (Jochen Blom)
10:30 – 11:00 Coffee Break
11:00 – 12:00 EDGAR hands-on (Jochen Blom, Sebastian Jaenicke)
12:00 – 12:30 Course evaluation & closing remarks (all hands)

During the afternoon of the last day participants are invited to discuss open questions or individual projects or data sets with the course experts.

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

Prerequisites:

None

Keywords:

Quality control, genome assembly, Microbial Genome Annotation, Comparative Genomics

Tools:
Galaxy, GenDB, ASA3P, EDGAR

Event type:
  • Workshops and courses
6th de.NBI Genomics training course https://tess.elixir-europe.org/events/6th-de-nbi-genomics-training-course Educators: Alexander Goesmann, Sven Griep, Oliver Rupp, Tobias Zimmermann, Oliver Schwengers, Andreas Hoek, Jochen Blom, Sebastian Jaenicke (BiGi) Date: 04.-06.05.2020 Location: Heinrich-Buff-Ring 58, Justus-Liebig-Universität, Gießen, Seminar Rm. 0024a Content: The first day will introduce software tools for the quality control of short read data. For conducting basic sequence read processing steps we will use our local Galaxy server. In the last session we will explain the basic approaches for genome assembly and run various genome assemblers: - Introduction to quality control - Automatic trimming of sequencing reads - The basics of genome assembly On the second day we will take a closer look at the genome assembly results. Afterwards, we provide a comprehensive introduction to microbial genome annotation. Available tools and algorithms for the different genome analysis and annotation steps will be explained and used within Galaxy. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline (ASA3P) that can be used to process thousands of genomes on a single day: - The basic principles of region and function annotation - Genome annotation tools and pipelines in Galaxy - Manual and distributed genome annotation using GenDB - Introduction to the ASA3P software 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 - Statistical analyses (core/pan/singleton development plots) - The public EDGAR database Agenda: Day 1: Quality control & genome assembly 13:00 – 13:15 Welcome & introduction (Alexander Goesmann) 13:15 – 13:30 Transfer of data sets 13:30 – 15:00 Read quality control & trimming incl. hands-on session (Sven Griep, Oliver Rupp) 15:00 – 15:30 Coffee Break 15:30 – 17:00 Introduction to genome assembly incl. hands-on session (Sven Griep, Oliver Rupp) Day 2: Microbial Genome Annotation 9:00 – 10:30 Introduction to microbial genome annotation (Alexander Goesmann) 10:30 – 11:00 Coffee Break 11:00 – 12:30 Genome annotation with Galaxy & GenDB hands-on session (Sven Griep, Oliver Rupp, Tobias Zimmermann) 12:30 – 13:30 Lunch 13:30 – 14:30 Introduction to ASA3P (Oliver Schwengers) 14:30 – 15:00 Coffee Break 15:00 – 17:00 ASA3P practical session (Oliver Schwengers, Andreas Hoek) 17:30 Optional: Tour to Gleiberg castle Day 3: Comparative Genomics 9:00 – 10:30 EDGAR (Jochen Blom) 10:30 – 11:00 Coffee Break 11:00 – 12:00 EDGAR hands-on (Jochen Blom, Sebastian Jaenicke) 12:00 – 12:30 Course evaluation & closing remarks (all hands) During the afternoon of the last day participants are invited to discuss open questions or individual projects or data sets with the course experts. Learning goals: On all three days the program includes extensive hands-on training to allow participants to get familiar with the presented software. Participants can bring their own datasets that fit the topics of the workshop. The data can be analyzed in the hands-on sessions. Prerequisites: None Keywords: Quality control, genome assembly, Microbial Genome Annotation, Comparative Genomics Tools: Galaxy, GenDB, ASA3P, EDGAR 2020-05-04 09:00:00 UTC 2020-05-06 17:00:00 UTC de.NBI Gießen, Gießen, Germany Gießen Gießen Gießen Germany [] [] [] workshops_and_courses [] []