Welcome to iGUIDE’s documentation

iGUIDE is a software pipeline for processing and analyzing double-strand DNA break events. These events may be induced, such as by designer nucleases like Cas9, or spontaneous, as produced through DNA replication or ionizing radiation. A laboratory bench-side protocol accompanies this software pipeline, and can be found (https://doi.org/10.1186/s13059-019-1625-3).

This documentation gives the reader an overview of the pipeline, including how to install and process a sample dataset. Processing a sample data set is broken into a few parts:

1. Developing a configuration file and sample information
2. Setting up a run directory and acquiring the sequence data
3. Initializing the pipeline and understanding the output

After processing sequencing run(s), additional evaluation and analysis can be performed by supplying supplemental data and combining specimen outputs from several runs.

To get started, see Quickstart Guide!