species abundacy calculation

Question

[vmicrobio]

Hi all,

I'm looking for ways and softwares to represent population diversity from fastq (for exemple x% E. coli, y% human, z% P. aeruginosa reads,...)

I intend to do a local blast on different databases then used GRAMMy

Do you guys have some recommendations, comments about this approach? Is it better to start with a with de novo approach before blast? How should I deal with my reads before blast?

Thanks!

[st.ph.n]

What type of data are your fastq?

[vmicrobio]

fastq were obtained by DNA sequencing of biological sample using Proton