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
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 www.putty.org
Mac/Linux: not required, terminal should be installed as standard
- FTP client - transfers files to/from the server
Windows/Mac/Linux - Filezilla Client www.filezilla-client.org
- Assembly viewer - visualisation of assemblies and coverage
Windows/Mac/Linux: Tablet ics.hutton.ac.uk/tablet/
- Sequence viewer - visualisation and manipulation of sequences and annotations
Windows/Mac/Linux: UGENE ugene.net