Reference based assembly with multiple references

Question

[deepti1rao]

I have a hybrid plant, generated from two distant varieties. I need to assemble its genome with NGS data. We have decided to do a reference based assembly, considering that its repeat content of 50% might be a problem for de novo assembly. Can I do it with multiple reference genomes? That is, with both parental genomes as references?

Answer 1

[Jean-Karim Heriche]

There are tools that can use multiple references e.g. Multi-CAR or Ragout.