Converting .fasta files to .gff3 files

Question

[chenbenyuan]

I'm trying to use Roary to do phylogenetic analysis.

It says "Alternatively you can use ncbi-genome-download to pull down the FASTA files and convert them to GFF3 with Prokka." in https://sanger-pathogens.github.io/Roary/

I already have all the .fasta file I need.

How am I supposed to convert it to .gff3 files?

Thank you.

[Sej Modha]

Roary manual states that you can use Prokka to convert fasta to .gff3

Answer 1

[sysbiocoder]

1. Convert fasta to BED first Check this How Do I Convert Fa Files To Bed Format? for that
2. use gff-tools (http://www.raetschlab.org/suppl/gff-tools) to convert BED to gff3

Answer 2

[Joe]

Prokka is a genome annotation pipeline. You aren't 'converting' the fasta as such. It's just the input to prokka which then adds all the annotations and features required.

Prokka then outputs various fasta files as well as a GFF3 and GBK.

You can then use those GFF3s as Roarys input.

I suggest you download and read the manual for prokka by Torsten Seemann