What is the best tool to recover nitrogen cycling genes from an annotated assembly?

Question

[robert.murphy]

I have annotated metagenomic assemblies and am wanting to recover genes involved in the nitrogen cycle. I have identified three tools to help me do this but I unsure how to go about selecting them most appropriate one:

1. Eggnog mapper
2. NCyc
3. KofamKoala

Does anyone have some insights into this?

[andres.firrincieli]

I would say NCyc only because already include protein sequences from eggNOG and KEGG (kofamKoala):

protein sequences for NCyc gene families were recruited from multiple public databases such as UniProt, KEGG, COG, eggNOG, and the SEED.

source

[robert.murphy]

This was my thinking but I guess i was being bad by thinking the more established tools could be better to use.

[andres.firrincieli]

As general rule, if your genome belongs to a lineage which have very few representative genomes you might want to use tools that assigns functions to sequence data by HMMER/HMMSEARCH (Kofamkoala)

[robert.murphy]

I am using unbinned metagenomic assemblies so that would mean Kofamkoala is potentially better?

NCyc allows the use of diamond, usearch and blast which are all alignment based I think (usearch is the only one I am unsure on)

[andres.firrincieli]

I am using unbinned metagenomic assemblies so that would mean Kofamkoala is potentially better?

Then use kofamkoala. Keep in mind that kofamkoala use protein sequences as input.

I have no experience with usearch

[robert.murphy]

I will give both a go as NCyC is build for metagenomic use. However I am assuming is better performance is due to the curated database rather than it search functions. so I imagine a combination of the two would be optimal?