ChangeLog

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)

v1.0.2 (February 15th, 2020)

  • Bugfix: UMItags set to FALSE will now process through to completion

  • Rebuild: Updated to build version 1.0.1

v1.0.1 (December 3rd, 2019)

  • Bugfix: Updated Gene set enrichment test within report

v1.0.0 (August 15th, 2019)

  • Complete support for BLAT and BWA aligners

  • Included a binning system to distribute workload into smaller loads

  • Implemented a version tracking system into the intermediate data files (incorp_sites)

  • Updated CLI with “hints” for snakemake processing

v0.9.9 (August 9th, 2019) - Additional updates

  • Implemented support for BWA aligner

  • Added tools (samqc) for working with other SAM/BAM output aligners as well

  • Switched iguide support code to iguideSupport R-package and added unit tests

  • Fixed bugs related to quoted table inputs (csv/tsv)

  • Implemented a method to skip demultiplexing, see documentation for setup

  • Resoved a number of issues identified, check GitHub for history!

v0.9.9 (June 10th, 2019)

  • 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 initiate a total reprocessing.

  • 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

v0.9.8 (April 19th, 2019)

  • 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

  • Added short stats-based report to be produced at the end of processing

  • Additional bugfixes.

v0.9.7 (March 6th, 2019)

  • Hotfix to workflow.

  • Changed ‘setup’ subcommand to python script based rather than snakemake.

  • Changed file organization.

v0.9.6 (March 5th, 2019)

  • Introduced process workflow steps: assimilate and evaluate

  • Assimilate aligned data and compare with targeting sequences

  • Incorp_sites now a core data object that can be combined across runs

  • 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 (February 19th, 2019)

  • 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)

v0.9.4 (January 30th, 2019)

  • Updated ‘report’ utility and formating. Custom templates now accepted. Included as subcommand, check with ‘iguide report -h’. PDF and HTML options report ‘nicely’ even when printed from either

  • Updated build to v0.9.2 to support new formating in report

  • Builds are constructed from spec files rather than yaml requirements

  • Included the ‘clean’ subcommand to reduce size of processed projects. After cleaning a project, only terminal data files will remain

v0.9.3 (January 11th, 2019)

  • Added ‘list_samples’ subcommand to list samples within a project.

  • Caught a few bugs and worked them out for smoother processing and reports.

v0.9.2 (January 7th, 2019)

  • Modified test dataset to run tests quicker and implemented CirclCI checking.

v0.9.1 (January 6th, 2019)

  • Fixed problematic install for first time conda installers.

v0.9.0 (January 4th, 2019)