Which strategy to get draft genome: rawread mapping or de novo assembly?

Question

[curiousbiologist]

Hi all,

I want to generate a clean consensus genome from fastq files. I also have a close reference I would like your opinion about what is the best strategy to get a draft genome: I can't determine from bibliography the best strategy: rawread mapping or de novo assembly? or both?

Is there a reference pipeline I missed?

Thanks a lot!

[Fabio Marroni]

You can give a look here

[curiousbiologist]

thank you Fabio! very usefull