What is the best tool to recover nitrogen cycling genes from an annotated assembly?
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:
Does anyone have some insights into this?
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robert.murphy •
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I would say NCyc only because already include protein sequences from eggNOG and KEGG (kofamKoala):
source
This was my thinking but I guess i was being bad by thinking the more established tools could be better to use.
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)
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)
Then use kofamkoala. Keep in mind that kofamkoala use protein sequences as input.
I have no experience with usearch
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?