v1.2.0

v1.2.0

Released on July 26th, 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

v1.1.2

Released on 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

Released on 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

• 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

• 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

v0.9.9

• Modified the assimilate + evaluate workflow
  • Assimilate now only includes reference genome data, meaning a cleaner intermediate file
  • Evaluate will now handle ref. gene sets and further analysis
  • This increases the modularity and consistancy of the workflow
• Revised the iGUIDE Report format to be more informational and clearer
• Revised a bit of the workflow to make reprocessing smoother
• Updated BLAT coupling script to be more memory efficient
• Fixed TravisCI testing!
• Changed stat workflow, now restarting analysis won't init a total reproc.

v0.9.8

• iGUIDE can now support non-Cas9 nucleases as well!
  • Implemented nuclease profiles into configs
  • Updated assimilation, evaluation, and reporting scripts
• Added default resources to allow simpler HPC processing
• Included flexible system for identifying on-target sites
  • Config can accept a range rather than a single site
  • Acceptable notation: chr4:+:397-416 and chr3:*:397
• Changed build nomenclature from v0.9.3 to b0.9.3
  • So as not to confuse with version
• Added 'summary' subcommand to generate a consise text-based report
  • Working in the same manner as 'report', can generate from config(s) or eval file
• Added short stats-based report to be produced at the end of processing
• Additional bugfixes.

v0.9.7

• Hotfix to workflow.
• Changed 'setup' subcommand to python script based rather than snakemake.
• Changed file organization.

v0.9.6

• Introduced process workflow steps: assimilate and evaluate
  • Assimilate aligned data and compare with targeting sequences
    • Core data object that can be combined across runs / projects
  • Evaluated data incorporates reference data and statistical models
    • A staple data object for reports and can be constructed from multiple runs
• Included new subcommands 'eval' and modified 'report'
  • report from either config(s) or eval dataset
• Cleaned up file structure
• Updated documentation in code and docs.
• Implemented accuracy and retention checks with simulation dataset.
• Updated simulation dataset with larger set to test analysis.

v0.9.5

• Updated demultiplexing to be more efficient and better HPC compatible.
• Added RefSeq Extended* reference gene sets
  • 'ext' includes curated, predicted, and other RefSeq sets
  • 'ext.nomodel' includes only curated and other RefSeq sets
• Incorporated resource allocation for job dependent memory consumption
  • Works great with HPC to specify memory requirements
• Streamlined input for report generation by only requiring config(s)