Genomes ML project

This repository contains files used in the LLM genome annotation project and the related manuscript.

Directories and files

Directories used for the manuscript

The following directories contained in this repository are directly relevant to the manuscript:

• infer_chromosome – files related to the chromosome 21 inference run and its analysis
• notebooks – Jupyter notebooks used for data postprocessing and plotting
• scripts – basic scripts for Evo and Evo 2 inference, used for the PoC gene annotation analysis

Directories related to the manuscript

The following directories are connected to the manuscript, but not directly relevant:

• extract_regions – a test of region extraction from FASTA based on GFF
• gene_boundaries – a test of gene boundary inference with Evo
• minihyena – a test of a small model based on Evo
• test_geneid – a test of using Evo output to improve geneid

Other directories

The following other directories are not related to the manuscript or purely technical:

• exploration – exploratory analyses done before the Evo analysis; not fully maintained
• logs – SLURM job stdout and stderr, not tracked

Most of the directories contain their own README with details.