# yeast_denovoassembly
Code used for the paper "Complete de novo assembly of yeast genomes using enzyme-free, dense optical genome mapping".
Data exists processed as SupplementaryData_matlabdata and Raw as SupplementaryData_Rawdata
To work, this requires DOGMA (https://gitlab.com/dnadev/dogma), and HCA (https://gitlab.com/dnadev/hca).

DOGMA requires SCAMP CLI for MP based pairwise comparisons and bargrouping (https://github.com/zpzim/SCAMP).

pipeline/ contains the core scripts used to load, process and assemble the CB-based OGM yeast data.
In short, the scripts here are recommended to be used as follows:

assembly_pipeline_yeast.m
1. Load raw kymographs
2. Merge neighboring barcodes
3. Masking of Peaks (extreme values) and Repetitive Finder
4. Pairwise comparison

paramertization.m

6. To get null-distribution parameters for bargrouping

bargrouping.m

7. To assemble the bargroups

figs/ contains scripts that can be used to use the bargroups generated to recreate parts of the main figures 

helper/  contains many helper scripts that are needed for scripts in figs and pipeline to work.

data/ contains .mat files with the already loaded data (not raw .tifs/.czi/.fasta)
