Releases: cnobles/iGUIDE
Releases · cnobles/iGUIDE
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
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
- Assimilate aligned data and compare with targeting sequences
- 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)
v0.9.4
- 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