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Changelog

Unreleased

ADDED

  • 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

FIXED

  • 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 bu output by @Colelyman in #602

CHANGED

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

REMOVED

v2.3.3 - Activity Fulton - 07/01/2025

ADDED

FIXED

  • Fix setting of 99%ile in negative direction for deletions plot in 90ac42a

CHANGED

  • Make fig_filename_root default to None, in which case the figure is shown interactively (e.g. in a jupyter notebook) in c2a10c4

  • Don't rerun if --no_rerun is set but --verbosity has changed in 6562a08

REMOVED

  • Remove warning for zipping nonexistant files in 3784ea5

v2.3.2 - Junction Salt - 01/16/2025

ADDED

  • New parameters, --flexiguide_gap_open_penalty and --flexiguide_gap_extend_penalty, to customize flexiguide alignment in #491

  • New parameter --halt_on_plot_fail so that errors and exceptions in plots don't fail silently in #494

  • New parameter --samtools_exclude_flag to customize the filtering of reads in #503

  • New documentation website at <docs.crispresso.com>.

  • Asymmetrical cut point by @kclem in #457

  • d3 plot enhancements by @trevormartinj7 in #459

  • Add flexiguide alignment parameters by @Colelyman in #491

  • Add pyproject.toml and support numpy v2 by @Snicker7 in #496

  • Add customizable samtools exclude flag by @Colelyman in #503

  • Add support for octal and comma separated samtools exclude flags (#113) by @kclem in #507

FIXED

CHANGED

v2.3.1 - Screen King - 05/13/2024

FIXED

CHANGED

REMOVED

v2.3.0 - Targeting Minato - 04/10/2024

ADDED

  • Guardrails (checking experimental conditions and raising warnings) by @Snicker7

  • Enable quantification by sgRNA by @kclem in #348

FIXED

CHANGED

v2.2.14 - Specific São Paulo - 08/10/2023

FIXED

v2.2.13 - With Montgomery - 07/28/2023

ADDED

FIXED

CHANGED

  • Don't start pool when only using single thread by @Colelyman in #302

  • Raise exceptions from within futures in plot_pool in a439f09

  • Enable CRISPRessoPooled multiprocessing when os allows multi-thread file append in ebb016d

  • Allow multiple overlapping sgRNA matches in reference (previous behavior was to only search for non-overlapping sgRNA sites in the reference sequence in 32e1e97

  • Assert correct input fastq file format in 7248ba8

  • Update plotCustomAllelePlot.py script for #292 by @kclem in #293

  • Clarify CRISPRessoWGS intended use by @Colelyman in #303

  • Case-insensitive headers accepted in CRISPRessoPooled e577318

  • Allow dashes in filenames in 712eb2a

  • Sort pandas dataframes by # of reads and sequences so that the order is consistent for testing by @Snicker7 and @Colelyman in #316

  • Update base_editor parameters in README and add Plot Harness by @Colelyman in #301

v2.2.12 - Protospace Utah - 02/01/2023

ADDED

  • Add deprecation notice in #260

  • Add snippet about installing CRISPResso2 via bioconda on Apple silicon in #274

FIXED

  • Fix CRISPRessoPooled bam input in #265

  • Fix deprecated numpy type names (fixes #269) in #270

  • CRISPRessoPooled custom header fix in #278

CHANGED

  • Status Updates + Pooled Mixed Mode Update in #279

v2.2.11 - Of Weber - 10/11/2022

FIXED

v2.2.10 - Overhangs Alameda - 09/15/2022

ADDED

  • Add --zip_output parameter to produce a zipped file report by @Colelyman and @Snicker7 in c80f828

  • Allow N's in bam output by @kclem in b0b7d41

  • Autodetect reference amplicons from interleaved fastq input

FIXED

  • Fix bug when comparing two samples with the same name in #228

  • Fix bug when name is provided instead of amplicon_name in pooled input file in #229

  • Fix for aggregate plots in Batch mode in #237

  • Fix loading of crispressoInfo from WGS and pooled in 49740ba

CHANGED

  • Parallel plot refactor in #247

  • Add plotly to dockerfile in b68a432

v2.2.9 - Long Surrey - 06/23/2022

ADDED

  • fastq_to_bam implementation in #219\
    • If the parameter --bam_output is provided, CRISPResso alignments will be written to a file called 'CRISPResso_output.bam' with the alignments in bam format. If the bowtie2_index is provided, alignments will be reported in reference to that genome. If the bowtie2_index is not provided, alignments will be reported in reference to a custom reference created by the amplicon sequence(s) and written to the file 'CRISPResso_output.fa'.\
    • This enables the viewing of CRISPResso alignments in other browsers (e.g., IGV). If no bowtie2_index is provided, the reference genome should be set to the produced 'CRISPResso_output.fa' file, and then the alignment bam can be loaded into IGV.

FIXED

  • Don't run global frameshift plot when there are no modified reads by @Colelyman in #226

CHANGED

  • CRISPRessobatch: put directory in quotes by @sshen8 in #222

v2.2.8 - Welcome to High Waikato - 05/13/2022

ADDED

  • Interactive plotly summary plots in CRISPRessoAggregate and CRISPRessoBatch for visualizing and comparisons

  • CRISPRessoPooled enhancement that allows the amplicons file to have a header and additional columns to be provided

  • CRISPRessoCompare generates a report of the number of significant reads at each base

CHANGED

v2.2.7 - Literature and Los Angeles - 02/11/2022

ADDED

  • Adds features for providing aligned bams as input to CRISPRessoPooled and for a faster demultiplexing when amplicons and genome are provided. The added parameters are:
    • --aligned_pooled_bam: Path to aligned input for CRISPRessoPooled processing. If this parameter is specified, the alignments in the given bam will be used to demultiplex reads. If this parameter is not set (default), input reads provided by --fastq_r1 (and optionally --fastq_r2) will be aligned to the reference genome using bowtie2. If the input bam is given, the corresponding reference fasta must also be given to extract reference genomic sequences via the parameter --bowtie2_index. Note that the aligned reads are paired-end seqenced, they should already be merged into 1 read (e.g. via Flash) before alignment.
    • --demultiplex_only_at_amplicons: If set, and an amplicon file (--amplicons_file) and reference sequence (--bowtie2_index) are provided, reads overlapping alignment positions of amplicons will be demultiplexed and assigned to that amplicon. If this flag is not set, the entire genome will be demultiplexed and reads with the same start and stop coordinates as an amplicon will be assigned to that amplicon.

FIXED

CHANGED

  • Improve performance by removing regex from indel location analysis by @Colelyman #182

  • Fastq output produced by --fastq_output now includes the inserted bases. Previously, a string like "DEL= INS=78(1) SUB= " would indicate a 1bp insertion at site 78. This update outputs strings like "DEL= INS=78(1+G) SUB= " with the insertion described as a plus character followed by the inserted bases. (2f84dd0)

  • Update ylabel_values -> y_label_values by @swrosati in #174

  • Allow mixed-case prime-editing input (e999079)

v2.2.6 - Basepairing Bern - 10/21/2021

ADDED

  • Add param --plot_center to allow custom plots centered at a given point in plotCustomAllelePlot script ecf23ef

  • Add unit tests 3e6c281

FIXED

  • Fix allele plotting error for plot 5 referring to uninitialized y_max variable 53197e6

  • Fix unicode errors for bam read/write 8196b6a

CHANGED

  • All sub-CRISPResso runs are run with 1 process in Batch, WGS, Pooled, etc. Because we added multiprocessing capabilities to CRISPResso (the plotting part) we thought it would be slick for CRISPRessoPooled to run sqrt(n_processes) CRISPResso processes with sqrt(n_processes) processes each. Unfortunately, sqrt(n) isn't a really useful number for the number of processes people usually run (e.g. 2 or 3 or even 8), and a lot of the CRISPResso processing isn't enabled to take advantage of multiprocessing (e.g. the alignment step), so processes were being wasted. So we reverted back to having n_processes CRISPResso processes, each with 1 process. a923a7c

  • Convert columns in nucleotide count and modification tables to numeric for PE analysis cabebbe

  • Make loggers module-specific so matplotlib debug doesn't get spewn out in the CRISPResso log c2bdd96

REMOVED

  • Remove version checks for numpy and seaborn 90b43ea

v2.2.5 - Immunity from Bonneville - 09/22/2021

FIXED

  • Fixes bug when sequencing reads are much longer than the given reference sequence.

v2.2.4 - Mutant Maricopa - 09/09/2021

ADDED

  • This release adds an additional parameter --assign_ambiguous_alignements_to_first_allele. For ambiguous alignments, setting this flag will force them to be assigned to the first (as provided by the references -a first and then -e second) amplicon. Thus, no reads will be discarded as 'ambiguous' and all reads will be counted once in the analysis.

CHANGED

  • Batch summaries are produced for amplicons present in only one sample.

v2.2.3 - Collateral Cardston - 08/30/2021

FIXED

  • Fixes database_id bug

v2.2.2 - Large Honolulu - 08/20/2021

FIXED

  • For some reason some of the previous commits resolving problems with filterFastqs weren't picked up in v2.2.1. So I'm hoping they'll be included here.

v2.2.1 - Sequence Length Salt Lake - 08/20/2021

FIXED

  • More unicode bug fixes for filtering fastqs

CHANGED

  • CRISPRessBatch now outputs summary of splicing/frameshift mutation status

v2.2.0 - Matches Sanpete - 08/13/2021

CHANGED

  • Python 3 release

    • Incorporates updates and changes from python2 up to this point

    • Adds multiprocessing to CRISPRessoBase to parallelize image generation to speed up results

      • CRISPRessoBatch, CRISPRessoPooled, and CRISPRessoWGS allocate processes to sub-CRISPResso commands so that sqrt(n_processes) sub-commands are run, each with sqrt(n_processes) unless plotting is turned off (via --suppress_report or --suppress_plots in which case n_processes are run, each with 1 process.

    • The crispresso_info dictionary containing run information is saved as json so it can be read across versions of python and by other programs (e.g. R). The dict structure of the object has also been changed to be more navigable and hierarchical.

    • Because of changes to crispresso_info, this version of CRISPResso will not be able to finish incomplete runs (e.g. checkpointing of CRISPRessoPooled) that were started by previous python2 versions of CRISPResso, or aggregate or access information from previous runs (e.g. using CRISPRessoAggregate, CRISPRessoCompare, or the custom python plotting scripts in scripts). However, even if we were to have stuck with pickle format for crispresso_info, the python2 and python3 versions were incompatible anyway. So we figured this was a good time to move toward a better format.

v2.1.3 - Lentiviral Cache - 06/29/2021

FIXED

  • Fixes bug for CRISPRessoPooled analyzes of many amplicons where samtools sort writes status updates that can't be parsed as reads.

v2.1.2 - Single Guide Washington - 06/23/2021

ADDED

  • Addition of a script for custom allele plotting 947fbab

CHANGED

  • Updates to CRISPRessoPooledWGSCompare, used for comparing multiple amplicons in CRISPRessoWGS or CRISPRessoPooled experiments 48d6c87
    • CRISPRessoPooledWGSCompare now produces html report linking to sub-CRISPRessoCompare reports

v2.1.1 - Nicking Hancock - 05/22/2021

ADDED

  • This release incorporates changes to make bowtie2 alignment in CRISPRessoPooled more permissive 4dc9e7, and remove duplicate rows in the Alleles_frequency_table.txt due to reads being in the forward or reverse direction 0e08cd0.

CHANGED

  • When given a genome file, CRISPRessoPooled aligns reads to the genome using the Bowtie2 aligner. The legacy parameters were somewhat strict. The new parameters reflect the 'default_min_aln_score' parameter in allowing for substantially more indels and mismatches than previous.
    • The parameter --use_legacy_bowtie2_options_string has been added to use the legacy settings. Otherwise, the bowtie2 alignment settings will be calculated as follows:
    • --end-to-end - no clipping, match bonus -ma is set to 0
    • -N 0 number of mismatches allowed in seed alignment
    • --np 0 where read (or ref have ambiguous character (N)) penalty is 0
    • --mp 3,2 mismatch penalty - set max mismatch to -3 to coincide with the gap extension penalty (2 is the default min mismatch penalty)
    • --score-min L,-5,-3*(1-H) For a given homology score, we allow up to (1-H) mismatches (-3) or gap extensions (-3) and one gap open (-5). This score translates to -5 + -3(1-H)L where L is the sequence length

v2.1.0 - Knockout Lake - 03/23/2021

CHANGED

  • Starting in version 2.1.0, insertion quantification has been changed to only include insertions completely contained by the quantification window. To use the legacy quantification method (i.e. include insertions directly adjacent to the quantification window) please use the parameter --use_legacy_insertion_quantification

  • In Prime Editing mode pegRNA spacer sequences given in the incorrect orientation are no longer tolerated

  • HDR: Ambiguous alignments don't contribute to the plot 4g (except when --expand_ambiguous_alignments is provided) --fastq_output now also writes alignment scores and alignments for every read

v2.0.45 - 12/30/2020

ADDED

  • CRISPRessoAggregate can be used to aggregate multiple completed CRISPResso runs.

v2.0.44 - 11/17/2020

CHANGED

  • Improvements in inferring quantification windows across amplicons/alleles.

v2.0.43 - 11/07/2020

ADDED

  • Add ticks to appropriate plots

  • New parameter --plot_histogram_outlier to plot 100% of data

FIXED

  • Update the function of histograms

  • By default 99% of data is shown in plots, now 100% of data is written to data files.

v2.0.42 - 09/30/2020

FIXED

  • Fixed % character in CRISPRessoPooled arg string

v2.0.41 - 09/30/2020

ADDED

  • Added --fastq-out parameter to report the CRISPResso analysis separately for each read. Note that this should be used with caution. I'm still trying to figure out what information should be reported for each read, and what format it should be in. Open to feedback on this issue!

FIXED

  • WGS parallelization mode bug fixed

CHANGED

  • WGS and Pooled summary figures scale height based on the number of entries so that they are legible in html reports.

v2.0.40 - 07/09/2020

CHANGED

  • Prime editing updates - scaffold parameter is now called --prime_editing_pegRNA_scaffold_seq. Guide names with spaces produce file names with hyphens instead of spaces

v2.0.39 - 07/07/2020

ADDED

  • Batch mode supports bam and multiple quantification windows

v2.0.38 - 07/01/2020

ADDED

  • Add new paramter --annotate_wildtype_allele to annotate wildtype alleles on the allele plots

  • Input can now be read from bam using the parameter --bam_input and (optionally) --bam_chr_loc to use the reads in the bam at this location as input.

  • An output bam is produced with an additional soace-separated field prefixed by c2 (e.g. c2:Z:ALN=Inferred CLASS=Inferred_MODIFIED MODS=D47;I0;S0 DEL=56(47) INS= SUB= ALN_REF=TTGGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGGCATGGCCCCATTCGCACGGCTCT----------------------------------------------- ALN_SEQ=ACACCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGA-----------------------------------------------TCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGGCATGGCCCCATTCGCACGGCTCTGGAGCGGCGGCTGCACAACCAGTGGAGGCAAGAGGGCGGCTTTGGGC). Note that the alignment details (location, cigar string, etc) are not modified.. this may be done in the future). Bam file input cannot be trimmed or pre-processed with quality filtering.

CHANGED

  • Prime editing scaffold incorporation is now more accurate (looks for the scaffold sequence at the expected position directly after the extension sequence). A plot showing the number of bases matching the scaffold, as well as insertions after the extension sequence, and a data file with these numbers is produced. Added parameter --prime_editing_pegRNA_scaffold_min_match_length to define the minimum length required to classify a read as 'Scaffold-incorporated'

  • Renamed split_paired_end parameter to --split_interleaved_input for interleaved input

  • Auto mode now considers 5000 reads to detect amplicon sequences

  • Update output when reporting missing files -- only lists first 15 files in the current directory and directory of input parameter

  • --reference https instead of http

v2.0.37 - 05/09/2020

ADDED

  • Max processors can be used in WGS and Pooled modes by setting -p max

  • Prime editing analysis can be performed by specifying the parameters: --prime_editing_pegRNA_spacer_seq --prime_editing_pegRNA_extension_seq and optionally --prime_editing_pegRNA_extension_quantification_window_size --prime_editing_pegRNA_scaffold_sequence --prime_editing_nicking_guide_seq with a summary shown in the report

  • Extended read analysis data available with --write_detailed_allele_table flag

CHANGED

  • CRISPRessoPooled demultiplexing is performed in parallel and with reduced filesystem demand

  • N's don't count as substitutions

  • Nucleotide plots are shaded when the nucleotide matches the reference sequence

  • sgRNA improvements: sgRNA annotations are plotted on multiple lines if they overlap sgRNAs can have their own cut site and quantification window size

v2.0.34 - 04/06/2020

ADDED

  • Pooled Set flag to skip reporting problematic regions

v2.0.33 - 04/03/2020

CHANGED

  • Plotting computation window is shaded

  • Parallelization and checkpointing of CRISPRessoWGS and Pooled

  • Increase of alignment efficiency of CRISPRessoPooled amplicons in genome +amplicons mode

v2.0.32 - 02/25/2020

CHANGED

  • Plotting updates, dsODN detection, and general improvements and bug fixes.

v2.0.31 - 09/26/2019

ADDED

  • Add custom post-processing plot functions for allele tables

FIXED

  • Fix CRISPRessoPooled handling of chromosomes with underscores

CHANGED

  • Update dependency requirements

v2.0.30 - 07/02/2019

ADDED

  • Add nucleotide summary for batch mode

FIXED

  • Fix bug for reporting amplicons with no reads

CHANGED

  • Case-insensitive checking for guides

v2.0.29 - 05/30/2019

CHANGED

  • By default, the html report is created on the outside of the output folder, so if the output is: CRISPResso_on_SAMPLE/ the html report will be at CRISPResso_on_SAMPLE.html

  • This functionality can be reverted to place the report inside of the output folder using the parameter --place_report_in_output_folder which will place the html report at: CRISPResso_on_SAMPLE/CRISPResso2_report.html

v2.0.28 - 05/24/2019

ADDED

  • Standardize file names

  • Add CRISPREssoCompare output html

CHANGED

  • CRISPRessoBatch guide-specific output are plotted as separate plots

  • Standardize window definitions (plot window and quantification window specify the distance from the cut site to the edge of the window, so the entire window is 2*plot window)

v2.0.27 - 04/05/2019

Added

  • Add reports for pooled and WGS

  • Add Batch pickle info

CHANGED

  • More precise plotting of cleavage cut site and quantification window

  • Bioconda updates

v2.0.26 - 03/06/2019

Added

  • Add report display name, remove paths from stored files, fix sgRNA plot, CRISPRessoPooled report HTML, add citation to report

v2.0.25 - 02/21/2019

Added

  • Add inferring of guides

v2.0.24 - 02/13/2019

Changed

  • Update docker, setup.py

v2.0.23 - 01/24/2019

Added

  • Add manifest.in

v2.0.22 - 01/23/2019

Changed

  • Change license location, license update

v2.0.21 - 01/22/2019

Changed

  • Detangled root location dependency from params

v2.0.20b - 01/22/2019

Changed

  • Prepare for bioconda integration