prokka --metagenome vs prodigal -c

[thierryjanssens]

The #--metagenome option does not result in the same behaviour as leaving out -c in the standalone prodigal version (tested with --kingdom Viruses).
Is there an option to include this as a new feature in the next version of prokka? This would be instrumental in the annotation of scaffold from a fragmented metagenome.

[tseemann]

I will consider it, but Prokka is not really designed for metagenomes.

[apcamargo]

Given that Prokka has a --metagenome option, I'd expect that partial gene sequences would be predicted. Maybe Prodigal's -c argument could not used when executing prokka with the --metagenome argument.

@tseemann do you think this would be detrimental for the downstream steps in Prokka's pipeline?

[jfourquet2]

Hi, we are potentially interested by using Prokka into our metagenomics analysis. We have the same issue with the partial genes which aren't predicted when we run prokka. Do you know if an option can be added to prokka in order to run Prodigal without -c option (when Prokka is used with or without --metagenome option) ? Thanks in advance for your answer !

[jfourquet2]

Hi,
I get on to @tseemann again for this issue, because we are very interested to use the -c option of Prodigal in Prokka. Do you know if it can be add as an option ? Thanks a lot in advance for you answer !

[xiaorongsmile]

I use the prokka to annotation the contigs fasta file after megahit assembly, the file size is 271,840,558bp, it will takes 135 minutes for one sample, is this normal, or should i not do this with prokka?