I've been searching around to find some good resources on metagenomic shotgun analysis but I can't really find any. I've read the biostars handbook section but it mostly covers 16S analysis. I'm specifically interested in long read (a la Nanopore) metagenomic sequence assembly.
I'm a newbie to this field, and from what I can tell, a generic assembly pipeline would look something like FastQC -> CANU -> some sort of unsupervised binning software -> RACON and then on to classifying and such.
In theory my goal is, I want to be able to go out into the woods with a minION, sequence some random soil bacteria, and be able to tell what bacteria it is, what it does, and also be able to identify any novel bacterial genomes present.
Am I on the right track here and can anyone point me in the direction of good resources, or have advice?