Workshop: Mitochondrial metagenomics: theory and practice

The workshop demonstrated basic techniques for mitochondrial genome assembly and annotation, and illustrated the power of mitogenomes in phylogenetics, biodiversity research and population genetics. The instructors for this Workshop were: Prof. Alfried P. Vogler (Imperial College London, UK), Dr. Thomas J. Creedy (Imperial College London, UK) and Dr. Massimiliano Babbucci (University of Padova, Italy).
In total, 35 participants from 12 different institutions attended the theoretical introduction and the practical session.

Date: 11-12 December 2017

Venue:  Royal Museum for Central Africa, Leuvensesteenweg 13, 3080 Tervuren, Belgium.


Monday 11th. 14:00 - 17:00

Plenary lecture "Mitochondrial metagenomics"

Tuesday 12th. 09:30 - 17: 00

Hands-on sessions:

Session 1a: De novo assembly of a whole mitochondrial genome from illumina paired sequencing reads

  • Introduction to assembly and the linux command line
  • Quality control, adapter trimming and read pairing
  • Mitogenome assembly using two different types of assemblers

Session 1b: Assembly interrogation and annotation

  • Viewing and assessing assembly quality
  • The effects of variation of assembly parameters
  • Annotating assembly using local and web tools

Session 2a: Assembling with sparse and low quality data

  • Selection of reference sequences
  • Assembly to a reference sequence
  • Viewing and annotating incomplete mitogenomes

Session 2b: Mitochondrial metagenomics

  • Assembly of mixed sequence libraries using multiple assemblers
  • Meta-assembly of multiple results
  • Contig identification

For the practical sessions, a few applications needed to be installed:

  • SSH client

Windows: PuTTY

Mac/Linux: not required, terminal should be installed as standard

  • FTP client - transfers files to/from the server

Windows/Mac/Linux - Filezilla Client

  • Assembly viewer - visualisation of assemblies and coverage

Windows/Mac/Linux: Tablet

  • Sequence viewer - visualisation and manipulation of sequences and annotations

Windows/Mac/Linux: UGENE



Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith