De Bruijn Graph Assembly
Requirements
Before diving into this slide deck, we recommend you to have a look at:
- Sequence analysis
- Quality Control: slides slides - tutorial hands-on
K-mers? 
- To be able to use de Bruijn graphs, we need reads of length L to overlap by L-1 bases.
- Not all reads will overlap another read perfectly.
- Read errors
- Coverage "holes"
- Not all reads are the same length (depending on technology and quality cleanup)
To help us get around these problems, we use all k-length subsequences of the reads, these are the k-mers.
SPAdes 
- de Bruijn graph assembler by Pavel Pevzner's group out of St. Petersburg
- Uses multiple k-mers to build the graph
- Graph has connectivity and specificity
- Usually use a low, medium and high k-mer size together.
Performs error correction on the reads first
Maps reads back to the contigs and scaffolds as a check
Under active development
Much slower than Velvet
- Should be used in preference to Velvet now.
keypoints Key points
We learned about how the choice of k-mer size will affect assembly outcomes
We learned about the strategies that assemblers use to make reference genomes
We performed a number of assemblies with Velvet and SPAdes.
You should use SPAdes or another more modern assembler than Velvet for actual assemblies now.
Thank You!
This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!
| Author(s) |
 
Simon Gladman
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| Reviewers |
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Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.