I have a bundle of sequence data need to be annotated. I want to try prokka annotation pipeline for this activity. (http://www.vicbioinformatics.com/software.prokka.shtml), but I have no idea how to run this. If any one can give me a some detailed in put, is highly appreciated.
Thank you,
Regards,
Amal.
Hi Amal,
I think it is all out there on the internet. There are two ways to go about this..
1. You could simply follow the tutorial here - https://github.com/tseemann/prokka/blob/master/README.md
2. You could register for an Illumina BaseSpace account and use the app on https://basespace.illumina.com/apps/590590
Personally I would go for option 1 which is pretty straightforward!
Good luck!
Hi Amal,
You have a 3rd option. If you don't have enough expertice with linux you can use online tools based on galaxy server (https://orione.crs4.it/).
Just upload your sequence and annotate it with Prokka.
Best regards,
Fernando
Hi Amal,
I've recently begun the same thing (40 genomes). I've been doing it by command line, and I've found this script to be particularly helpful for submitting the sequences to prokka:
for file1 in * #(i.e. *.fasta)
do
out=${file1%%} #add output suffix here if desired (i.e._prokka_output)
prokka file1 --outdir $out
done
or all in one line:
for file1 in * ; do out=${file1%%} ; prokka file 1 --outdir $out ; done \;
to be sure that this will result in the correct calculation, use 'echo' in front of 'prokka', and this should show you the intended output.
Hope this helps!
Hi Amal
Devon has mentioned a good point using 'for' loop in Linux to repeat running a large number of samples. A simpler one-liner command (Prokka beginner level) will be (k here is the variable):
for k in FILE1.FASTA FILE2.FASTA FILE3.FASTA; do prokka $k --outdir "$k".prokka.output;echo $k;done
This will print the filename after finish annotation on the standard output (the screen). You prokka annotated files will be in the folders FILE1.prokka.output (FILE1 here is your assemblies).
You can do this to get all the options to add on to your annotation after this software is installed:
prokka -h
However using Prokka will require basic Linux skills - otherwise you can try Galaxy (I have not used this before). Hope this helps!
you can actually use Proksee, a new version of cgview to annotate your genome using Prokka.
Are there any basic tutorials on prokka available
If available please send me here
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools