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Genomics in Environmental Microbiology (2016)

ECTS credits:


Course parameters:
Language: English
Level of course: PhD
Time of year: October 17-28, 2016
Hours reading and preparation prior to course: 45 hours
Hours in class/group work: 80 hours
Capacity limits: 12 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 (bacteria or archaea) to an assembled and annotated genome. Students work with sequence data obtained from genomic DNA that they submit before the course begins.


Week 2: Comparative microbial genomics
Students will learn how to compare assembled and annotated microbial genomes from a functional and evolutionary perspective.


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. A final presentation of each student's independent comparative genomics project. Independent projects are determined by the students themselves, where each student defines their own question to be answered by comparing genomes (either genomes sequenced during the class or genomes obtained from databases).

Course contents:
Students submit DNA from a bacterial or archaeal strain or single-amplified genome about six weeks before the course begins. Students determine what strain they wish to work on, and we encourage students to choose a strain closely related to their PhD research. The DNA is then sequenced, and data provided to students on the first day of the course.

Class time is divided into group lecture/discussion time each morning and 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. Assemble and annotate the genome of a bacterium or archaeon from raw sequencing data to a publication-quality annotation.
  2. Test a hypothesis by comparing microbial genomes.

 Topics covered include:

  • Sequencing methods
  • Mirobial genomics study design
  • UNIX command line tools for bioinformatics
  • Assembly of microbial genomes
  • Gene calling
  • Gene identification
  • Gene identification based on sequence alignment
  • Gene identification based on patterns, profiles, and hidden markov models
  • Genome annotation pipelines
  • Whole genome phylogeny and comparative genomics
  • Genome pathway prediction and comparison
  • Submitting genomes to NCBI
  • Obtaining whole genomes from metagenomes
  • Single-cell genomics
  • Gene expression and regulation monitoring and prediction
  • Horizontal gene transfer

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, Aarhus University


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. If students don't have other publication plans for their genomes, then this will generally be a short manuscript submitted to Genome Announcements (


October 17-22 and 24-28, 8:30 - 16:30


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


Deadline for application is June 1, 2016.

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. 500-word description of the strain or single-amplified genomic DNA you plan to sequence during the course. Include your motivation for sequencing this strain, a description of how it relates to your PhD project, and any available information, or citations of information, about its provenance (when and how it was/will be isolated, how it came to your lab).

Submit these items by email to Ian Marshall, e-mail: and Lars Schreiber, e-mail: by June 1, 2016.

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

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Revised 05.11.2018