Question: Adding read information to dBG nodes
1
gravatar for R.Fuentes
2.2 years ago by
R.Fuentes10
Philippines
R.Fuentes10 wrote:

Hi,

I'm trying to use dbgh5 and Minia to assemble paired reads + single reads. But I'm not sure how to retrieve the read information after the assembly. Is there a way I can use the graph or I need to map reads to the sequence generated? I read Biostars' answers related this but I'm not sure if newer dbgh5 and minia version allow easier solution to this. Thank you!

Roven 

minia gatb • 601 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by R.Fuentes10
1
gravatar for Rayan Chikhi
2.2 years ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k wrote:

Hi,

Read information is still not included in the newer versions. You'll have to map the reads to the sequences generated.. Minia forgets about the reads very early in the assembly process (right after k-mer counting). We don't have plans to include read information in the future. Most de Bruijn graph assemblers also don't keep that information during the initial assembly phase, they just re-map the reads to the graph at a later stage.

 

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Rayan Chikhi1.2k

Thanks, Rayan!

ADD REPLYlink written 2.2 years ago by R.Fuentes10
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