# Break Sites Prediction

SSBlazer can accurately predict the probability of single strand breaks at each nucleotide position within a DNA sequence provided in FASTA format.

## Running Prediction

In order to annotate Single-Strand Break (SSB) sites on a genome, you can utilize the `genome_pred.py` script that is included in our toolset. This script reads in a FASTA file, performs the prediction of SSB sites, and outputs these predictions in BED format:

```
python genome_pred.py --in chr1.fa --out chr1_annotated.bed --batchsize 128
```

In this command:

* `--in chr1.fa` specifies the input FASTA file for the genome to be annotated.
* `--out chr1_annotated.bed` specifies the output BED file where the annotations will be written.
* `--batchsize 128` sets the batch size to 128 for processing. You can adjust this value depending on the available resources on your machine.

The script will run and output a BED file (`chr1_annotated.bed` in this case) containing predicted break probabilities for the supplied genome.

### Visualizing the Output

You can visualize the BED file output using Integrative Genomics Viewer (IGV). IGV is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

Follow the instructions on the[ IGV website ](https://igv.org/doc/desktop/)to install the software if you haven't already done so, and then load your BED file to view the annotated SSB sites on your genome.

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