Question: Can I upload several Genbank files to RAST?
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gravatar for Alec Watanabe
12 months ago by
Alec Watanabe60 wrote:

Greetings,

I have been using RAST for bacterial genome annotation for about 1 year. In this time I've only worked with a few genomes, but now I am working with a huge list of bacterial genomes (precisely 108 genomes). What I want to know is: is there any way that I can submit all these 108 genomes (Genbank files) to the RAST server at the same time? Submitting one by one would be really time consuming and I would do that only if there is really no other option. The subsequent program (PanWeb) will be used for pan-genome analysis and it requires EMBL files standardized by RAST as input files. Do you have any suggestion on how I can manage to process these files? Maybe using another annotation server? Maybe another strategy?

Many thanks!

Alec

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ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 12 months ago by Alec Watanabe60
0
gravatar for jrj.healey
12 months ago by
jrj.healey13k
United Kingdom
jrj.healey13k wrote:

Use a commandline implementation of RAST, or my advice would be to switch to prokka. Web servers are never as versatile.

ADD COMMENTlink modified 12 months ago • written 12 months ago by jrj.healey13k

Thanks for your reply! I've been reading about the command line option of RAST and it will for sure facilitate the process shall I use it. If I were to switch to prokka, do you recommend any software for pan-genome analysis? I'd need to test it, but I'm not completely sure that PanWeb would accept the output file of prokka, although it does accept gbk.

ADD REPLYlink written 12 months ago by Alec Watanabe60

The program Roary is designed to take the output of prokka for several genomes and produce core genome/accessory genome analyses. I can’t remember off the top of my head whether it gives you back the pangenome specifically, but that information would be extractable if not regardless (there are other tools that escape me at the moment that should do it too).

ADD REPLYlink written 12 months ago by jrj.healey13k

PGAP is best for pangenome analysis, and RASTtk surely can proceed with several genomes. PROKKA is also best like RASTtk for annotation.All the best.

ADD REPLYlink written 11 months ago by k.kathirvel93200

I’ve not used PGAP, but it is older and less highly cited than roary. I’d want to see some specific performance indicators to suggest PGAP is “best”.

ADD REPLYlink written 11 months ago by jrj.healey13k
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