Workshop: Mitochondrial metagenomics: theory and practice

Date: 11-12 December 2017

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

Programme:

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 hands-on sessions, we will accept a maximum number of 30 participants. We still have a few slots available and we will select at least one person per research unit.

For the practical sessions, you'll only need to have a few applications installed on your laptop :
 

  • 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

                  

 

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