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iGUIDE - improved Genome-wide Unbiased Identification of Double-strand DNA break Events

CircleCI Documentation Status DOI

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:

v1.2.0 (July 13th, 2025)

  • Updated build to R-base 4.4 (overdue) and rebuilt environment files.
  • Due to the large jump in many package versions, minor modifications needed to be made the the software, making many changes incompatible with prior scripts.
  • Special Note: ReadName patterns in configs need to be double escaped (ie. [\\w]). Please see simulation config files for examples.

v1.1.2 (April 17th, 2025)

  • Resolved a bug dealing with factor levels during auxiliary workflow solutions.
  • Added a second simulation data set (B) and labeled the original simulation data set (A).
  • Expanded tests to cover auxiliary workflow solutions.

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