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Genomics in Environmental Microbiology (2015)

Name of course:

Genomics in Environmental Microbiology

ECTS credits:


Course parameters:

Language: English

Level of course: PhD

Time of year: 19 - 30 October 2015

No. of contact hours/hours in total incl. preparation, assignment(s) or the like:

Hours in class/group work: 80 hours

Hours reading prior to and during course: 30 hours

Capacity limits: 10 participants

Objectives of the course:

To train students in the sequencing, de-novo assembly, annotation, and analysis of genomes obtained from environmental isolates, single-cell whole genome amplification, or metagenomics.

Learning outcomes and competences:

The course is divided into two weeks, each with a different focus:


Week 1: The fundamentals of environmental microbial genomics.

Students will learn how to turn extracted DNA from an environmental isolate or single-cell whole genome amplification to an assembled and annotated genome. Students work with sequence data obtained from genomic DNA that they submit before the course begins.


Week 2: So you have a microbial genome; now what?

Students will learn how to take assembled and finished genomes and predict metabolic pathways, how to compare genomes from a functional and evolutionary perspective, and how to navigate the nuances of single-cell genomics, metagenomics, and metatranscriptomics.

Compulsory programme:

1) Attendance in class for eight hours every day during the ten days of the class.

2) A report describing each student's assembly and annotation of a microbial genome (students are encouraged to submit genomic DNA relevant to their own research a week before the class begins for sequencing). This takes the form of a manuscript for submission to the journal Genome Announcements (

3) An oral presentation (delivered by groups of 3-4 students) of the group's independent project. Independent projects are selected by the students, but must include use of an analysis tool or approach described in course contents points 6-10.

Course contents:

Class time is divided into group lecture/discussion time each morning and individual or group bioinformatics work (with instructors available) in the afternoon. The majority of knowledge transfer will be in the form of assigned reading or videos ahead of each lecture (i.e. that students will be expected to carry out before the course begins or in the evenings), with class mornings dedicated to explaining and reinforcing concepts introduced during individual study. Group bioinformatics work each afternoon will give students time to carry out bioinformatic analyses leading to their written report and final oral presentation. Guest lectures by microbial genomics researchers will also be included.

At the end of the course, the student should be able to:

1) Choose the most appropriate sampling, sample preparation, and sequencing methods for microbial genomics or metagenomics projects

2) Use UNIX command line tools to assess and manipulate genomic data, and carry out the analyses taught throughout the course

3) Choose an appropriate genome assembly software tool and use at least one of the possible options

4) Identify a gene's function as best possible based on analysis of its sequence

5) Annotate a microbial genome using an automated software tool and explain the weaknesses and strengths of various annotation tools and approaches

6) Know how genome-driven pathway prediction tools predict metabolic pathways

7) Know how microbial genomes are compared from both a functional and evolutionary perspective

8) Understand key differences between the annotation of genomes and metagenomes and explain the weaknesses and strengths of various metagenomic annotation tools and approaches

9) Explain different approaches to obtaining whole genomes from metagenomes and single cells

10) Understand how genomes are used as a framework for understanding other 'omics' data (i.e. transcriptomic and proteomic data)

11) Carry out at least one of the analyses described in outcomes 6-10


Master's-level knowledge in microbiology and molecular biology, for example from a master's degree in biology, molecular biology, or bioinformatics.

Name of lecturers:

Ian Marshall, Lars Schreiber

Type of course/teaching methods:

Seminar-style discussion sessions, guided group bioinformatics lab work, some lecture-style teaching


Various current scientific literature from the fields of bioinformatics and microbiology.

Course homepage:


Course assessment:

Attendance, written report, oral presentation


Department of Bioscience

Special comments on this course:

As a condition of attending this course, students commit to submitting a manuscript for publication to a peer-reviewed journal based on the sequence data generated and analysed with the instructors included as co-authors. Generally, this will be a short manuscript submitted to Genome Announcements (, but students have the option of submitting to another journal if the significance of the work justifies it.


19-23 and 26-30 October 2015, at 8:30 - 16:30.


Department of Bioscience, Aarhus University, Aarhus (room to-be-announced)


Deadline for application is 1 August 2015. Information regarding admission will be sent out no later than 5 August 2015.

For registration please submit your CV, a max. 200-word description of your PhD project and your motivation for taking the class, and a max. 200-word description of the sequencing project you plan on carrying out during the class. Submit these items by email to Ian Marshall ( and Lars Schreiber ( by 1 August 2015.

If you have any questions, please contact course instructors Ian Marshall or Lars Schreiber at the email addresses above.

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Revised 20.06.2016