How to convert gff to gbk format. I have the assembled fasta also

Question

[robert.murphy]

I have annotated a fungal genome with Augustus which outputs a GFF file fomat. I need the now run this genome through some downstreams tools that need GBK input as they for biosynthetic gene clusters within the sequence. How can I convert this GFF file to GBK?

Answer 1

[Ram]

Please search the site before you ask a question: Gff3 + Fasta To Genbank (Augustus Training Set)

[robert.murphy]

I did and have seen this thread but the script the person mentions to use is not designed for standalone and has no guidance of how to operate it as such so I don't know how to use it. Plus with the thread being 9 and a half years old I thought it might be good to get an update of any better methods or new tools that I have not been able to find whilst looking :)

[Ram]

Yes, there is a good chance that things have improved dramatically in 9 years.

the script the person mentions to use is not designed for standalone and has no guidance of how to operate it

I don't think that's the case. The post contains just an excerpt from the actual script, which is posted in its entirety on github and has a brief usage statement. Can you try the script and then let us know if you face a problem?

[robert.murphy]

I am trying the script now but am stuck at what seems to be a requierd option called max-size-of-gene-flanking-DNA. I am not really sure what it is meant to be.

[Ram]

Just so we're clear, are we talking about the same script? (gff_to_genbank.py from here)?

[robert.murphy]

Ah opps I though you were refering to the Augustus perl script gff2gbSmallDNA.pl from here. I will try the script you just linked.