Recommendation list

blastn for NT or CAMERA
blastn for silva database (SE)
SOAPdenovo (PE)
MetaWRAP binning

Note "SE": For single-end read, "PE": For paired-end read, "GE": Genome explorer which is our original genome browser.
It is necessary to register to analyze your own data.
: The popular pipeline or the latest one that the developer recommend.
Notice: Unrecomend not a tool used by the pipeline but the workflow of the pipelie.

References:

• Nature. 2012 Sep 13;489(7415):250-6. doi: 10.1038/nature11553.