This was brought up during the discussion with @idoerg and @mortonjt . The most competent tools seem including 1) GeneMark, 2) Glimmer, and 3) Prodigal. The first option we choose here, prodigal, is based on literature. A paper shows Prodigal performs better, according to their benchmark:
Pati,A., Ivanova,N.N., Mikhailova,N., Ovchinnikova,G., Hooper,S.D., Lykidis,A. and Kyrpides,N.C. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Meth, 7, 455–457.
This is open for discussion and plugin other tools if they are better for gene calling.
This was brought up during the discussion with @idoerg and @mortonjt . The most competent tools seem including 1)
GeneMark, 2)Glimmer, and 3)Prodigal. The first option we choose here, prodigal, is based on literature. A paper shows Prodigal performs better, according to their benchmark:This is open for discussion and plugin other tools if they are better for gene calling.