Question: Is there any open-source Illumina bacterial genome mapping and annotation website?
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gravatar for bioinf_ukraine
6 months ago by
bioinf_ukraine0 wrote:

Is there any open-source Illumina bacterial genome mapping and annotation website, using RAST or similar in an automated way. Need software codes to develop a similar service. Thank you.

ADD COMMENTlink modified 6 months ago by h.mon26k • written 6 months ago by bioinf_ukraine0

You can find NCBI's prokaryotic annotation pipeline here: https://github.com/ncbi/pgap . There is also Prokka: https://github.com/tseemann/prokka

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax69k

I have a Prokka, however I need to send a fasta contigs to the RAST via the Linux Shell or a Python code, is it possible somehow?

ADD REPLYlink written 6 months ago by bioinf_ukraine0

Looks like there is a way to batch submit jobs. Have you looked at this page?

Edit: Unfortunately the link for the submit script on that page appears to be broken.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax69k

NOTE: Comments verifying the authenticity of the post have been cleaned up.

ADD REPLYlink written 6 months ago by RamRS22k
0
gravatar for h.mon
6 months ago by
h.mon26k
Brazil
h.mon26k wrote:

The page http://www.theseed.org/servers/ mentions there is a package called "RASTserver.pm", you can search for this package and find more information. Also, the RAST blog has a post about the The RAST batch interface.

ADD COMMENTlink written 6 months ago by h.mon26k
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