Metagenomics data analysis

Metagenomics investigates the composition and function of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances in high-throughput sequencing technologies, and the increasing data sizes require efficient analysis methods and advanced computing approaches.

This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced.

The course consists of lectures and hands-on exercises. User-friendly analysis platforms META-pipe and Chipster are used in the exercises, so no programming skills are required, and the course is thus suitable for everybody.

  • META-pipe has been developed by ELIXIR-Norway, and it offers tools for pre-processing (Trimmomatic, FastQC), assembly (MegaHit), taxonomic classification (LCA-classifier), gene prediction (Glimmer/MGA), functional analysis (Blast, Priam, InterProScan) and visualization (Metarep). META-pipe analysis jobs use a Spark cluster in the cloud for computation.
  • Chipster offers over 360 analysis tools for different kinds of high-thoughput data. For community analysis of amplicon sequencing data it has tools for pre-processing (Prinseq, Trimmomatic, FastQC, Mothur), taxonomic classification (Mothur), and statistical analysis for marker gene studies (R packages vegan, rich, biodiversityR, pegas and labdsv).

The course material was prepared by the following people:

  • Nils Willassen, Espen Robertsen, Erik Hjerde, Inge Alexander Raknes (ELIXIR-Norway)
  • Rob Finn (EBI)
  • Anu Mikkonen (University of Jyväskylä)
  • Jenni Hultman, Petri Auvinen (University of Helsinki)
  • Jarno Tuimala (RS training)
  • Maria Lehtivaara, Kimmo Mattila, Eija Korpelainen (CSC)

Scientific topics: Metagenomics

Resource type: Video, course materials

Difficulty level: Beginner

Authors: Eija Korpelainen, Nils Peder Willassen, Espen Mikal Robertsen, Erik Hjerde, Rob Finn, Anu Mikkonen, Jenni Hultman, Petri Auvinen, Kimmo Mattila, Maria Lehtivaara, Jarno Tuimala

Contributors: Eija Korpelainen

Metagenomics data analysis https://tess.elixir-europe.org/materials/metagenomics-data-analysis This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos. The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity. Eija Korpelainen Metagenomics