iGUIDE - improved Genome-wide Unbiased Identification of Double-strand DNA break Events
Bioinformatic pipeline for processing iGUIDE and GUIDE-seq samples.
Description
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.
Changelog:
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