pré-assembly step in DeBruijn Graph

Question

[midox]

hello friends,

I need to know is that in the assembly with Berjuin Graph there is a pre-assembly step (reads low filtering, cleaning reads, ...) or the pre-assembly step is done after construction of the graph of Berjuin?

Thank you for your reply

Answer 1

[Renesh]

The de Bruijn graphs is a algorithm involved in constructing the continuous sequences. This algorithm used by most of the assembly tool as it is efficient for handling large number of reads (eg. Trinity).

Before performing assembly, you have to filter your sequence data for various contamination such as adapters, low quality bases and uncalled bases (N). This will help to reduce the number of low quality sequences and will give good assembled sequences.

[midox]

OK, thank you for your answer.
Thus it is necessary to make a phase of pre-assembly before using the DeBruijn Graph??

[Renesh]

Yes. Because your reads may have low quality bases and adapters contamination. This may create problem in forming overlap of k-mer by DeBruijn Graph.