Bioinformatic pipeline for processing iGUIDE and GUIDE-seq samples.

iGUIDE is a pipeline written in snakemake 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.

To get started, checkout the iGUIDE documentation at iGUIDE.ReadTheDocs.io.

v1.1.1 (December 16th, 2024)

• Added reference gene lists to ./genomes directory, as well as updated versions.
• Resolved bug associated with recovering multihit sites during analysis.
• Added option for Anaconda testing in test script to support custom installs. Try: bash etc/tests/test.sh iguide 1 anaconda with an anaconda install.
• Added functionality for more compatible gene lists between reference gene sets used for enrichment analysis.
• Updated sections of the documentation.

v1.1.0 (March 8th, 2020)

• Modified how samples designated as Mock are treated during the analysis
• Mock samples can now be indicated by "None" or "Control" as well (case-insensitive)
• Abundance can now be selected as [Read], [UMI], or [Fragment]{default} within config parameters and this selection will identify the abundance method used for analysis
• Added support for alternative UMI method (dx.doi.org/10.17504/protocols.io.wikfccw)

v1.0.0 (August 15th, 2019)

• Release of version 1.0.0!!!
• iGUIDE is a computational pipeline that supports the detection of DSBs induced by designer nucleases
• Aligner support for BLAT and BWA currently implemented, let us know if you would like to see others.
• Flexible pipeline processing built on Snakemake, supports a binning system to better distribute workflow for whichever system it is being processed on
• Documentation supporting a Quickstart and User Guide hosted by ReadTheDocs