maizegenetics/breeder-notebook repository overview

⁠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