README.md

Breeder Notebook

A Jupyter Docker Stack for plant scientists and breeders.

What's included?

This Docker image includes software broadly useful for bioinformaticians, with a specific focus on plant scientists and plant breeders.

If there is software that you think should be included here but isn't, please open an issue to discuss! You can also easily extend any of the existing Jupyter Docker Stacks with software for your specific case (that's what we did).

Buckler Lab Software

Software developed by members of the Buckler Lab:

• TASSEL
• The Practical Haplotype Graph
• rTASSEL and rPHG

Innovation Lab for Crop Improvement

Software developed by members of the Feed the Future Innovation Lab for Crop Improvement:

• BrAPI Helper JupyterLab extension that provides GUI for managing database connections to breeding management systems (e.g. BMS, BreedBase, GIGWA)
• Notebook templates (using JupyterLab Templates) providing instruction on common bioinformatics and data science pipelines for breeders

Common Bioinformatics Tools

• minimap2
• samtools & bcftools
• bwa (Burrow-Wheeler Aligner)

Programming Languages

The JupyterLab environment comes with kernels for the following:

• Python
• R
• Kotlin