Targeting Minato

Targeting Minato v2.3.0

Major changes:

• Flash and Trimmomatic are replaced with Fastp by @trevormartinj7, @Snicker7, and @Colelyman
• Guardrails (checking experimental conditions and raising warnings) by @Snicker7
• Failed runs are displayed with the error by @trevormartinj7

Minor changes:

• Replace link to CRISPResso schematic with raw URL in README by @Colelyman in #329
• Fix samtools piping by @Colelyman in #325
• Prime editing alignment params by @kclem in #336
• Fix for recent Matplotlib v3.8 by @mbowcut2 in #346
• Enable quantification by sgRNA by @kclem in #348
• Fix Matplotlib breaking change issue by @mbowcut2 in #352
• Fix assigning multiple qwc by @Snicker7 in #375
• Run unit tests via Github Actions and fix matplotlib character issue by @Snicker7 and @mbowcut2 in #386
• Remove future Pandas warnings and sort CRISPRessoCompare tables by @mbowcut2 and @Snicker7 in #389
• Fix interleaved fastq input in CRISPRessoPooled and suppress CRISPRessoWGS params by @Colelyman in #392
• Fix #367, reads only align to prime edited amplicon, not to reference by @mbowcut2 in #393
• Run integration tests on every push by @Snicker7 in #394
• Move read filtering to after merging in CRISPResso by @Colelyman in #397
• Fix the assignment of multiple quantification window coordinates by @Snicker7 in #403
• Decrease Docker image size and fix PE naming and parameter behavior by @Colelyman, @Snicker7 and @mbowcut2 in #404
• fix space character in README by @DennyDai in #400
• Fix Jinja2 undefined variables by @Colelyman in #417
  Full Changelog: v2.2.14...v2.3.0

Specific São Paulo

What's Changed

• CRISPRessoPooled
  • Fix missing ' in CRISPRessoPooled --demultiplex_only_at_amplicons
  • CRISPRessoPooled --compile_postrun_references bug fixes
• Prime editing quantification
  • Fix bug in prime-editing scaffold-incorporation plotting

Full Changelog: v2.2.13...v2.2.14

With Montgomery

What's Changed

This release improves parallel processing performance and increases flexibility in input file headers and output file naming conventions.

Major updates

• Parallelization updates
  • Don't start pool when only using single thread by @Colelyman in #302
  • Parallel plotting fix by @Colelyman and @kclem in 546446e and #286
  • 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

Minor updates:

• 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
• Add verbosity argument to CRISPRessoAggregate (#18) fixes #306 by @Colelyman in #307
• Clarify CRISPRessoWGS intended use by @Colelyman in #303
• Update plotCustomAllelePlot.py script for #292 by @kclem in #293
• Case-insensitive headers accepted in CRISPRessoPooled e577318
• Fix multiprocessing lambda pickling by @Colelyman in #311
• Allow dashes in filenames in 712eb2a

Full Changelog: v2.2.12...v2.2.13

Protospace Utah

What's Changed

• Add deprecation notice in #260
• Fix CRISPRessoPooled bam input in #265
• Add snippet about installing CRISPResso2 via bioconda on Apple silicon in #274
• Fix deprecated numpy type names (fixes #269) in #270
• CRISPRessoPooled custom header fix in #278
• Status Updates + Pooled Mixed Mode Update in #279

Full Changelog: v2.2.11...v2.2.12

Of Weber

What's Changed

• Fix batch quilt plot name by @Colelyman in #249
• Batch amplicon plots by @kclem in #251
• Fix typo of CRISPResssoPlot when plotting nucleotide quilt by @Colelyman in #250

Full Changelog: v2.2.10...v2.2.11

Overhangs Alameda

New Features

• 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

What's Changed

• Parallel plot refactor in #247
• Add plotly to dockerfile in b68a432

Minor Fixes

• 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

Full Changelog: v2.2.9...v2.2.10

Long Surrey

New Features

• 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.

Minor Fixes

• CRISPRessobatch: put directory in quotes by @sshen8 in #222
• Don't run global frameshift plot when there are no modified reads by @Colelyman in #226

Full Changelog: v2.2.8...v2.2.9

High Waikato

Welcome to High Waikato

New Features:

• 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

What's Changed

• minor bug fixes for plotCustomAllelePlot.py to work with Python3 by @dharjanto in #212
• Coerce ints in batch file checking by @Snicker7 in #200
• Large aggregation by @Colelyman in #192
• flexible pooled input by @Snicker7 and @kclem in #217

Full Changelog: v2.2.7...v2.2.8

Literature and Los Angeles

What's 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)
• 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.

Minor bug fixes:

• Fix deprecated pandas indexers (eea442a, f4b6cfc)
• Update ylabel_values -> y_label_values by @swrosati in #174
• Allow mixed-case prime-editing input (e999079)
• Fix int bug for CRISPRessoPooled n_reads (ef15cae)

Full Changelog: v2.2.6...v2.2.7

Basepairing Bern

Various improvements and bug fixes:

• Add param --plot_center to allow custom plots centered at a given point in plotCustomAllelePlot script (ecf23ef)
• 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)
• Remove version checks for numpy and seaborn (90b43ea)
• Fix allele plotting error for plot 5 referring to uninitialized y_max variable (53197e6)
• Fix unicode errors for bam read/write (8196b6a)
• 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)
• Add unit tests (3e6c281)

Full Changelog: v2.2.5...v2.2.6