Creating a GenomeSize.xml for a soybean genome

[brunabavelino]

Dear @tamsen
We are having a bad time here trying to understand how to make a GenomeSize.xml for the soybean genome assembly 2 (https://data.jgi.doe.gov/refine-download/phytozome?organism=Gmax&expanded=275). Our intention is to use it for running the DNA Amplicom module of the Local Run Manager v3 for SNP calling. Is there any simple way to make this file? ;D
Bruna

[tamsen]

Hi! Thanks for your interest in Pisces. Its so exciting to hear its involved in the soybean genome assembly! :)

1. Yes, you can use the CreateGenomeSizeFile executable to generate that file. See https://github.com/tamsen/Pisces/wiki/Pisces-Tools-5.3.0

2. You can get latest binaries here: https://github.com/tamsen/Pisces/releases/tag/v5.3.0.0

3. Can you please re-post your question here, https://github.com/tamsen/Pisces ? We are moving away from enterprise hosting.

Thanks!
Tamsen

[brunabavelino]

Hi, thank you very much for your help. I will be checking the documentation and binary files. Of course, I will be reposting the question here.
Best.

Bruna

[brunabavelino]

Hello, I would like to thank you again for your support and for your patience in helping me with the doubts I had regarding Pisces. I managed to do it thanks to your help. Thank you so much for your help and patience.
Hugs.
Bruna