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Assembly of metagenomic sequencing data

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Abstract

Metagenomics involves the extraction, sequencing and analysis of combined genomic DNA from entire microbiome samples. It includes then DNA from many different organisms, with different taxonomic background.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

  • Why metagenomic data should be assembled?
  • What is the difference between co-assembly and individual assembly?
  • What is the difference between reads, contigs and scaffolds?
  • How tools based on De Bruijn graph work?
  • How to assess the quality of metagenomic data assembly?

Learning Objectives

  • Describe what an assembly is
  • Describe what de-replication is
  • Explain the difference between co-assembly and individual assembly
  • Explain the difference between reads, contigs and scaffolds
  • Explain how tools based on De Bruijn graph work
  • Apply appropriate tools for analyzing the quality of metagenomic data
  • Construct and apply simple assembly pipelines on short read data
  • Apply appropriate tools for analyzing the quality of metagenomic assembly
  • Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome

Licence: Creative Commons Attribution 4.0 International

Keywords: Microbiome, assembly, metagenomics, microgalaxy

Target audience: Students

Resource type: e-learning

Version: 5

Status: Active

Prerequisites:

Introduction to Galaxy Analyses

Learning objectives:

  • Describe what an assembly is
  • Describe what de-replication is
  • Explain the difference between co-assembly and individual assembly
  • Explain the difference between reads, contigs and scaffolds
  • Explain how tools based on De Bruijn graph work
  • Apply appropriate tools for analyzing the quality of metagenomic data
  • Construct and apply simple assembly pipelines on short read data
  • Apply appropriate tools for analyzing the quality of metagenomic assembly
  • Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome

Date modified: 2024-11-26

Date published: 2022-12-05

Authors: Bérénice Batut, Polina Polunina

Scientific topics: Metagenomics, Microbial ecology, Sequence assembly

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