v2.1.6

CRISPRme v2.1.6 Release Notes

Description

This release introduces version 2.1.6 of CRISPRme, bringing significant updates, new features, and critical bug fixes. This version is designed to improve the performance and accuracy of off-target predictions and enhance the user experience in the CRISPRme ecosystem.

Key Features and Changes

🚀 New Features

• Support for GNOMAD v4.1 VCFs (joint VCFs included): CRISPRme now supports GNOMAD v4.1 datasets, including joint variant files, enabling more comprehensive analyses.
• Complete-test Function: A new complete-test function has been introduced for testing CRISPRme. This function provides a quick test for off-target prediction on a single chromosome, as well as a more detailed full-genome test.

🐛 Bug Fixes

• Fix 1: Corrected the handling of indels in off-target reporting, ensuring that only valid off-targets created by indels are accurately identified, eliminating false positives.
• Fix 2: Fixed a bug in the alternative alignments report, ensuring that all possible alignments for each off-target are accurately listed in the alternative alignments file.
• Fix 3: Resolved issues with the visualization of the Personal Card tab in CRISPRme's GUI and website, improving usability and clarity.
• Fix 4: Addressed a memory overflow issue during the merging of contiguous targets, ensuring more efficient performance and stability during large-scale analyses.

🛠 Enhancements

• Upgraded DockerHub version with the latest improvements and fixes.

Upgrade Instructions

To upgrade to version 2.1.6, follow these steps:

1. Create a new environment (if using mamba or conda):

   mamba create -n crisprme
   mamba activate crisprme
   mamba install crisprme=2.1.6
   

2. Docker: Pull the latest version from DockerHub:

   docker pull pinellolab/crisprme:latest
   

Documentation Updates

• The README.md has been updated to reflect the latest changes, including detailed documentation for the following functions:
  • complete-search
  • complete-test
  • targets-integration
  • gnomAD-converter
  • web-interface
  • generate-personal-card

Linked Issues

• Closes #67, #62, #64 related to this release.

Full Changelog: v2.1.5...v2.1.6

v2.1.5

Summary

This release addresses several issues and brings enhancements to CRISPRme:

1. Bug Fixes:
     - Resolved a bug that prevented alternative targets created by indels from being reported.
     - Fixed an issue that blocked the tool from reporting all alternative alignments found for each site.

2. Performance Improvements:
     - Enhanced memory usage and reduced computational time by optimizing the target clustering procedure.

3. New Features:
     - Added support for GnomAD v4.0 VCF files.

What's Changed

• Gnom AD v4.0 VCF support (#58)
• Indels report bug fix and targets clustering optimization (#61)

Full Changelog: v2.1.4...v2.1.5

v2.1.4

Summary

This release enables to start CRISPRme's test via command line, providing users with a more streamlined and efficient testing pipeline. Additionally, this release resolves a bug encountered during indels analysis.

What's Changed

• Fix Indels Analysis Bug: addresses a critical bug related to indels analysis (#49 ).

• Introduce Test Functionality as Command Line: Users can now easily test CRISPRme's functionality via command line, streamlining the testing process and improving usability (#53).

• Fix error on conda build for crisprme test (#55 and #56)

Full Changelog: v2.1.3...v2.1.4

v2.1.3

Summary

This release enables to start CRISPRme's test via command line, providing users with a more streamlined and efficient testing pipeline. Additionally, this release resolves a bug encountered during indels analysis.

What's Changed

• Fix Indels Analysis Bug: addresses a critical bug related to indels analysis (#49 ).
• Introduce Test Functionality as Command Line: Users can now easily test CRISPRme's functionality via command line, streamlining the testing process and improving usability (#53).
• Fix error on conda build for crisprme test (#55 and #56)

Full Changelog: v2.1.2...v2.1.3

CRISPRme - v2.1.2

Summary

• custom targets sorting while merging close targets (command line options --sorting-criteria-scoring and --sorting-criteria)
• print current CRISPRme version from command line
• Fix bug on targets filtering by chromosome, when searching only the reference genome

What's Changed

• Fix guide sorting mm bulges (#46)
• Fix reference only search (#47)

Full Changelog: v2.1.1...v2.1.2

CRISPRme - v2.1.1

This release includes:

• Detailed error tracing (redirected to log_verbose.txt)
• Stop CRISPRme execution when any step fails
• Resume CRISPRme analysis from the failed step (until off-targets search)

update to allow multi-thread post processing

• introduced user defined multi-thread count for many post-processing operations
• solved bug when no annotation file in input

bug fix and zenodo release update

fixed bug with bed type input
new release for zenodo stable

update to reflect website changes

fixed bug with PAM file path
update GUI
fixed bug in visualization
fixed stability of website
increased number of concurrent jobs
update names and download files available
zip files at execution time

release with fix and update gui

v2.0.7

fix bug in indels and snp analysis with misaligned targets