bakta is renaming input contigs in its outputs

[splaisan]

Dear Oliver,

I ran bakta using your latest docker (bakta 1.8.2) and found when visualising various results in IGV that the original Flye contigs had been renumbered/renamed by bakta in the annotation files to arbitrary 1/2/3 indices.

Is this intended and how can I prevent it? I have mapped data which I want to show side by side with annotations and this is not going to work well.

Thanks for your feedback

input fasta assembly:

contig_1    6356    10  60  61
contig_3    3971673 6482    60  61
contig_4    87384   4044360 60  61

bakta fna file

contig_1    6356    138 60  61
contig_2    3971673 6736    60  61
contig_3    87384   4044742 60  61

[splaisan]

Maybe I can use --replicons and a minimalist table with only 'original sequence id' and the same 'new sequence id' to force the names to the original flye contig names?! Just found the comment in the doc😅 and will try this tomorrow Maybe an option '--keep_names' with defaut to false could help here for other people with the same issue.

[oschwengers]

Hi @splaisan, If you only would like to keep the original contig IDs, then simply setting --keep-contig-headers should work.

There are some other parameters that might be interesting/helpful. You can find a full description here: https://github.com/oschwengers/bakta#usage

Please, do not hesitate to ask, if there are any further questions.

[splaisan]

How could i mis this one, i definitely have to read the usage more carefully 🤣

[oschwengers]

You're welcome ;-)