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Changelog

v2.3.4 - Amplicon Upolu - 04/23/2026

ADDED

  • Add --coding_seq_name parameter to provide custom names for coding sequences, fixing an issue where using the full coding sequence in filenames produced paths that were too long by @mbowcut2 in #627

  • Add an amino acid nucleotide quilt plot by @mbowcut2 in #552

  • Add scripts/reconstituteReads.py to generate FASTQ from CRISPResso2 output by @kclem in a800762 and cd79dcc

  • Add an UpSet plot to represent bystander edits for Base Editing analyses by @mbowcut2 in #554

  • Allow for messages to be served via CRISPResso reports by @Colelyman in #583

  • Add a plot that shows the distribution of homology scores for reads by @mbowcut2 in #600

  • Add the option to output edits in VCF format by @trevormartinj7 and @Colelyman in #613

    • To use the feature, add --vcf_output and --amplicon_coordinates parameters, and all of the edits within the quantification window will be compiled into a VCF file called CRISPResso_output.vcf in your results directory.

  • Add support for pixi for dependency management and installation by @Colelyman in #618

FIXED

  • Fix amplicon_name check in Jinja template to avoid undefined variable errors by @mbowcut2 in #627

  • Fix enrichment ordering and allele sorting in CRISPRessoCompare plots by @Colelyman in #626

  • Fix a crash when --suppress_plots is used with amino acid plots by @mbowcut2 in #624

  • Fix fastp options to respect user-provided --fastp_options_string and fix fastp read merge flags for unmerged reads by @kclem in #591 and #608

  • Fix Python package discovery in setup.py and pyproject.toml by @Colelyman in #616

  • Fix base editing plot naming by @mbowcut2 in #564

  • Fix the x_lim settings on plot 3b by @kclem in 56bd430

  • Fix parsing the CRISPResso2_info.json in CRISPRessoPooled by @kclem in #558

  • Forced cloned include_idxs to be np.arrays by @kclem in da4badb

  • Fix the link to the CRISPResso cup in reports (so that SSL works correctly) by @Colelyman in #571

  • Fix the quantification of deletions at the second position of the sequence by @Colelyman in #574

  • Fix an issue with unaligned reads not being reported correctly when writing BAM output by @trevormartinj7 in #578

  • Fix an issue where quantification window coordinates we not being correctly inferred by @Colelyman in #598

    • This issue is present when there is a single quantifcation window coordinate provided and multiple amplicons. What happens is CRISPResso aligns the second amplicon to the first and then infers what the quantification window coordinates should be based on the alignment. A regression was introduced where the inference of the quantification window coordinates for the second amplicon was no longer correct. This change fixes the regression and brings the behavior back to match that of v2.2.9.
    • If you don't set quantification window coordinates and don't use multiple amplicons, there is no need for this fix and therefore no change in behavior.

  • Fix a SyntaxWarning for an unescaped sequence in a matplotlib function by @Colelyman in #600

  • Fix a bug during --bam_output when there is an unaligned read, the remainder of the reads will not be output by @Colelyman in #602

  • Fix a bug when an sgRNA aligns before the start of an exon by @mbowcut2 in #628

  • Fix CRISPRessoPooled handling for non-string chromosome IDs and gene annotation with integer chr_id, and fix a missing-last-chunk bug in pooled processing by @kclem and @Colelyman in #635, c2d0c5c, and 85e4763

  • Fix coords_r handling for prime editing extension sequences that end at the end of the reference by @Colelyman in #615

CHANGED

  • Vendor the UpSet plot implementation, removing the external upsetplot dependency by @mbowcut2 in #623

  • Improve the sizing and display of the Base Editing UpSet plot and add percentages by @mbowcut2 in #586

  • Add plot diff comparisons and integration tests via pixi by @Snicker7 and @Colelyman in #622 and #626

  • Add expanded unit tests by @Snicker7 in #620

  • Apply safe ruff linting fixes by @Snicker7 in #621

  • Extract get_prime_editing_guides into a separate function for improved code organization by @kclem in #592

  • Update the base Docker image to mambaorg/micromamba:2.3.3 and remove dependency on Anaconda defaults channel by @Colelyman in #575

  • Change the guardrails interface to a dropdown that is a more minimal design by @Snicker7 in #619

  • Add explicit tool name handling for CRISPRessoPooledWGSCompare report generation by @Colelyman in #630

REMOVED