Adding read information to dBG nodes

Question

[R.Fuentes]

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

Answer 1

[Rayan Chikhi]

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.

[R.Fuentes]

Thanks, Rayan!