Question: Is there any open-source Illumina bacterial genome mapping and annotation website?
0
gravatar for bioinf_ukraine
4 weeks 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 4 weeks ago by h.mon23k • written 4 weeks 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 4 weeks ago • written 4 weeks ago by genomax62k

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 4 weeks 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 4 weeks ago • written 4 weeks ago by genomax62k

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

ADD REPLYlink written 4 weeks ago by RamRS20k
0
gravatar for h.mon
4 weeks ago by
h.mon23k
Brazil
h.mon23k 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 4 weeks ago by h.mon23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1313 users visited in the last hour