Hi,
I am contacting you about differents options of Prokka.
I ran Prokka 1.14.6 on the same sample with these two different command lines:
prokka --metagenome --noanno --rawproduct --outdir PROKKA_sampleId --prefix samplieId assembly_file.fasta --centre X --compliant --cpus 8prokka --metagenome --outdir sampleId --prefix sampleId assembly_file.fasta --centre X --compliant --cpus 8
Firstly, I wanted to well understand the option --noanno used into the second comand line (which is described in the help of Prokka but not into this github page). Is this option allow to deactivate all the five steps described into the paragraph 2.2 Annotation of Prokka paper (are there entirely past?)? I'm referring to steps (1) optional BLAST+ blastp for user-provided protein database, (2) BLAST+ against UniProt, (3) BLAST+ against RefSeq, (4) use of HMMER package and (5) annotate no matches with hypothetical protein. When I am using this option, Prokka is running much faster and I have not EC numbers and COG. Is Prokka much faster because it didn't run all the 5 steps previously described? Is this absence of EC number and COG well related to the presence of --noanno option?
I used also in this second command line the option --rawproduct which (if I well understand) allows to write the name of the product (which is hypothetical protein when -noanno is used on the same command). Is it correct?
Thanks lot in advance for your answer !
Hi, I am contacting you about differents options of Prokka. I ran
Prokka 1.14.6on the same sample with these two different command lines:prokka --metagenome --noanno --rawproduct --outdir PROKKA_sampleId --prefix samplieId assembly_file.fasta --centre X --compliant --cpus 8prokka --metagenome --outdir sampleId --prefix sampleId assembly_file.fasta --centre X --compliant --cpus 8Firstly, I wanted to well understand the option--noannoused into the second comand line (which is described in the help of Prokka but not into this github page). Is this option allow to deactivate all the five steps described into the paragraph2.2 Annotationof Prokka paper (are there entirely past?)? I'm referring to steps (1) optional BLAST+ blastp for user-provided protein database, (2) BLAST+ against UniProt, (3) BLAST+ against RefSeq, (4) use of HMMER package and (5) annotate no matches withhypothetical protein. When I am using this option, Prokka is running much faster and I have not EC numbers and COG. Is Prokka much faster because it didn't run all the 5 steps previously described? Is this absence of EC number and COG well related to the presence of --noanno option? I used also in this second command line the option--rawproductwhich (if I well understand) allows to write the name of the product (which ishypothetical proteinwhen-noannois used on the same command). Is it correct? Thanks lot in advance for your answer !