Taxonomy for Database

[dcdanko]

Not an issue with the program but looking for a bit of advice.

I'm building a BURST database based on refseq-microbial for use with SHOGUN. How did you build the example genome taxa file?

I'm guessing this is pretty straightforward.

Thank you!

https://github.com/knights-lab/SHOGUN/blob/master/shogun/tests/data/genomes.small.tax

[GabeAl]

Hi David,

Maybe this could be of some use to you?

https://github.com/knights-lab/BURST/blob/master/embalmlets/bin/Readme_utils.txt

Specifically the part about annotating the taxonomy. Hope this helps!

On Thu, Aug 9, 2018, 10:09 AM David C Danko notifications@github.com wrote:

Not an issue with the program but looking for a bit of advice.

I'm building a BURST database based on refseq-microbial for use with SHOGUN. How did you build the example genome taxa file?

I'm guessing this is pretty straightforward.

Thank you!

https://github.com/knights-lab/SHOGUN/blob/master/shogun/tests/data/genomes.small.tax

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[dcdanko]

This works very well thank you.

What about the sheared_bayes.fixed.txt file? Is this something I need to generate for a specific database?

[bhillmann]

Yes you can create a custom sheared_bayes.fixed.txt for a custom database. It isn't quite streamlined yet though. I should be able to add those updates soon. The scripts exists currently here.

The steps are shear the database with shear_db.py, align the sheared file to the database, and parse the b6 file with parse_shear.py