Question: pré-assembly step in DeBruijn Graph
0
gravatar for midox
5.7 years ago by
midox260
Tunisia
midox260 wrote:

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

debruijngraph assembly • 970 views
ADD COMMENTlink modified 4.9 years ago by Biostar ♦♦ 20 • written 5.7 years ago by midox260

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

ADD REPLYlink written 5.7 years ago by midox260

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.

ADD REPLYlink written 5.7 years ago by Renesh1.8k
2
gravatar for Renesh
5.7 years ago by
Renesh1.8k
United States
Renesh1.8k wrote:

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.

ADD COMMENTlink written 5.7 years ago by Renesh1.8k
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