Shotgun_metagenomics

Preprocessing

Assembly

metaspades and megahit are two decent options
Current version of MetaSPAdes can only assemble a single sample - pity as it produces slightly better assemblies than megahit.
Megahit uses a lot less (~1/4) memory than MetaSPAdes

Functional analysis

Functional bins

Genomic bins

Taxonomy assignment

Metakallisto/kracken/centrifuge?

Assembly free binning