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Thought this might be of interest to various folks. I made a Twitter moment regarding a discussion about microbial genome annotation methods.
Microbial Genome Annotation Methods
4 thoughts on “Microbial Genome Annotation Methods Twitter discussion”
No one mentions Glimmer because perhaps they think it is too ‘old’ – but it works great, as it has for 20 years now, and we still maintain it at https://ccb.jhu.edu/software/glimmer/. Glimmer finds 98-99% of the protein coding genes in a ‘naked’ bacterial assembly, including draft genomes, as we showed in a series of papers from 1998 to 2007.
Although every time I see Glimmer I am reminded that MS Word used to always try to correct it to “Gummer”
RAST when I have huge number of genomes but in combination with KEGG (using HMM search) and COG/Pfam. PROKKA or eggNOG when I have small number of genomes, or to go more in detail on some specific genomes.
PROKKA and eggNOG if I have to annotate one or few genomes; RAST in combination with KEGG (using HMM) and COG/Pfam if the number of genomes is high.