- Course overview
- Search within this course
- Introduction
- Course materials and software
- Metagenomics bioinformatics – course introduction
- Quality control and host decontamination
- The European Nucleotide Archive
- Tools to assemble short reads
- MGnify services
- MGnifyR
- Binning and MAG generation
- ENA metagenomics standards
- MGnify MAG resources
- Strain resolution
- Tools for comparative metagenomics
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Tools to assemble short reads
Rob Finn introduces various bioinformatics tools and processes that can be used in the assembly of short-read metagenomic data. This talk covers how the assembly tools/algorithms work, some computational considerations when performing assembly, what makes a good assembly, and some of the advantages and disadvantages of co-assembly. The assembly process results in the creation of de novo assembled contigs that can then be submitted to ENA and/or further processed through binning, towards generating MAGs.
Practical
You can try out the process for assembling short-read metagenomic data by following this practical tutorial. This exercise will cover how to begin assembling reads into contigs, the basic analysis of assembled data, and then how co-assembly can also be undertaken on the experimental data.
All the necessary information you need for this practical can be found below:
- Practical guide:
- This practical uses the same Docker container from the first session, therefore you should be able to start straight away