CRISPRessoPooled Parameters
Fastq R1
-r1, --fastq_r1
Help: First fastq file
Type: str
Fastq R2
-r2, --fastq_r2
Help: Second fastq file for paired end reads
Type: str
Amplicon Sequence
-a, --amplicon_seq
Help: Amplicon Sequence (can be comma-separated list of multiple sequences)
Type: str
Amplicon Name
-an, --amplicon_name
Help: Amplicon Name (can be comma-separated list of multiple names, corresponding to amplicon sequences given in --amplicon_seq
Type: str
Default: Reference
Amplicon Min Alignment Score
-amas, --amplicon_min_alignment_score
Help: Amplicon Minimum Alignment Score; score between 0 and 100; sequences must have at least this homology score with the amplicon to be aligned (can be comma-separated list of multiple scores, corresponding to amplicon sequences given in --amplicon_seq)
Type: str
Default Minimum Alignment Score
--default_min_aln_score, --min_identity_score
Help: Default minimum homology score for a read to align to a reference amplicon
Type: int
Default: 60
Expand Ambiguous Alignments
--expand_ambiguous_alignments
Help: If more than one reference amplicon is given, reads that align to multiple reference amplicons will count equally toward each amplicon. Default behavior is to exclude ambiguous alignments.
Type: bool
Default: False
Assign Ambiguous Alignments To First Reference
--assign_ambiguous_alignments_to_first_reference
Help: If more than one reference amplicon is given, ambiguous reads that align with the same score to multiple amplicons will be assigned to the first amplicon. Default behavior is to exclude ambiguous alignments.
Type: bool
Default: False
Guide Seq
-g, --guide_seq, --sgRNA
Help: sgRNA sequence, if more than one, please separate by commas. Note that the sgRNA needs to be input as the guide RNA sequence (usually 20 nt) immediately adjacent to but not including the PAM sequence (5' of NGG for SpCas9). If the PAM is found on the opposite strand with respect to the Amplicon Sequence, ensure the sgRNA sequence is also found on the opposite strand. The CRISPResso convention is to depict the expected cleavage position using the value of the parameter '--quantification_window_center' nucleotides from the 3' end of the guide. In addition, the use of alternate nucleases besides SpCas9 is supported. For example, if using the Cpf1 system, enter the sequence (usually 20 nt) immediately 3' of the PAM sequence and explicitly set the '--cleavage_offset' parameter to 1, since the default setting of -3 is suitable only for SpCas9.
Type: str
Guide Name
-gn, --guide_name
Help: sgRNA names, if more than one, please separate by commas.
Type: str
Flexiguide Seq
-fg, --flexiguide_seq
Help: sgRNA sequence (flexible) (can be comma-separated list of multiple flexiguides). The flexiguide sequence will be aligned to the amplicon sequence(s), as long as the guide sequence has homology as set by --flexiguide_homology.
Type: str
Default: None
Flexiguide Homology
-fh, --flexiguide_homology
Help: flexiguides will yield guides in amplicons with at least this homology to the flexiguide sequence.
Type: int
Default: 80
Flexiguide Name
-fgn, --flexiguide_name
Help: flexiguide name
Type: str
Discard Guide Positions Overhanging Amplicon Edge
--discard_guide_positions_overhanging_amplicon_edge
Help: If set, for guides that align to multiple positions, guide positions will be discarded if plotting around those regions would included bp that extend beyond the end of the amplicon.
Type: bool
Default: False
Expected HDR Amplicon Sequence
-e, --expected_hdr_amplicon_seq
Help: Amplicon sequence expected after HDR
Type: str
Exon Specification Coding Sequence/s
-c, --coding_seq
Help: Subsequence/s of the amplicon sequence covering one or more coding sequences for frameshift analysis. If more than one (for example, split by intron/s), please separate by commas.
Type: str
Config File
--config_file
Help: File path to JSON file with config elements
Type: str
Default: None
Minimum Average Read Quality (phred33 Scale)
-q, --min_average_read_quality
Help: Minimum average quality score (phred33) to keep a read
Type: int
Minimum Single bp Quality (phred33 Scale)
-s, --min_single_bp_quality
Help: Minimum single bp score (phred33) to keep a read
Type: int
Minimum bp Quality or N (phred33 Scale)
--min_bp_quality_or_N
Help: Bases with a quality score (phred33) less than this value will be set to 'N'
Type: int
File Prefix
--file_prefix
Help: File prefix for output plots and tables
Type: str
Sample Name
-n, --name
Help: Output name of the report (default: the name is obtained from the filename of the fastq file/s used in input)
Type: str
Suppress Amplicon Name Truncation
--suppress_amplicon_name_truncation
Help: If set, amplicon names will not be truncated when creating output filename prefixes. If not set, amplicon names longer than 21 characters will be truncated when creating filename prefixes.
Type: bool
Default: False
Output Folder
-o, --output_folder
Help: Output folder to use for the analysis (default: current folder)
Type: str
Verbosity
-v, --verbosity
Help: Verbosity level of output to the console (1-4) 4 is the most verbose
Type: int
Default: 3
Split Interleaved Input
--split_interleaved_input, --split_paired_end
Help: Splits a single fastq file containing paired end reads into two files before running CRISPResso
Type: bool
Default: False
Trimming Adapter
--trim_sequences
Help: Enable the trimming with fastp
Type: bool
Default: False
Trimmomatic Command
--trimmomatic_command
Help: DEPRECATED in v2.3.0, use --fastp_command
Type: str
Default: None
Trimmomatic Options String
--trimmomatic_options_string
Help: DEPRECATED in v2.3.0, use --fastp_options_string
Type: str
Flash Command
--flash_command
Help: DEPRECATED in v2.3.0, use --fastp_command
Type: str
Default: None
Fastp Command
--fastp_command
Help: Command to run fastp
Type: str
Default: fastp
Fastp Options String
--fastp_options_string
Help: Override options for fastp, e.g. --length_required 70 --umi
Type: str
Min Paired End Reads Overlap
--min_paired_end_reads_overlap
Help: Parameter for the fastp read merging step. Minimum required overlap length between two reads to provide a confident overlap
Type: int
Default: 10
Max Paired End Reads Overlap
--max_paired_end_reads_overlap
Help: DEPRECATED in v2.3.0
Type: str
Default: None
Stringent Flash Merging
--stringent_flash_merging
Help: DEPRECATED in v2.3.0
Type: bool
Default: False
Quantification Window Size
-w, --quantification_window_size, --window_around_sgrna
Help: Defines the size (in bp) of the quantification window extending from the position specified by the '--cleavage_offset' or '--quantification_window_center' parameter in relation to the provided guide RNA sequence(s) (--sgRNA). Mutations within this number of bp from the quantification window center are used in classifying reads as modified or unmodified. A value of 0 disables this window and indels in the entire amplicon are considered. Default is 1, 1bp on each side of the cleavage position for a total length of 2bp. Multiple quantification window sizes (corresponding to each guide specified by --guide_seq) can be specified with a comma-separated list.
Type: str
Default: 1
Quantification Window Center
-wc, --quantification_window_center, --cleavage_offset
Help: Center of quantification window to use within respect to the 3' end of the provided sgRNA sequence. Remember that the sgRNA sequence must be entered without the PAM. For cleaving nucleases, this is the predicted cleavage position. The default is -3 and is suitable for the Cas9 system. For alternate nucleases, other cleavage offsets may be appropriate, for example, if using Cpf1 this parameter would be set to 1. For base editors, this could be set to -17 to only include mutations near the 5' end of the sgRNA. Multiple quantification window centers (corresponding to each guide specified by --guide_seq) can be specified with a comma-separated list.
Type: str
Default: -3
Exclude bp From Left
--exclude_bp_from_left
Help: Exclude bp from the left side of the amplicon sequence for the quantification of the indels
Type: int
Default: 15
Exclude bp From Right
--exclude_bp_from_right
Help: Exclude bp from the right side of the amplicon sequence for the quantification of the indels
Type: int
Default: 15
Use Legacy Insertion Quantification
--use_legacy_insertion_quantification
Help: If set, the legacy insertion quantification method will be used (i.e. with a 1bp quantification window, indels at the cut site and 1bp away from the cut site would be quantified). By default (if this parameter is not set) with a 1bp quantification window, only insertions at the cut site will be quantified.
Type: bool
Default: False
Ignore Substitutions
--ignore_substitutions
Help: Ignore substitutions events for the quantification and visualization
Type: bool
Default: False
Ignore Insertions
--ignore_insertions
Help: Ignore insertions events for the quantification and visualization
Type: bool
Default: False
Ignore Deletions
--ignore_deletions
Help: Ignore deletions events for the quantification and visualization
Type: bool
Default: False
Discard Indel Reads
--discard_indel_reads
Help: Discard reads with indels in the quantification window from analysis
Type: bool
Default: False
Needleman Wunsch Gap Open
--needleman_wunsch_gap_open
Help: Gap open option for Needleman-Wunsch alignment
Type: int
Default: -20
Needleman Wunsch Gap Extend
--needleman_wunsch_gap_extend
Help: Gap extend option for Needleman-Wunsch alignment
Type: int
Default: -2
Needleman Wunsch Gap Incentive
--needleman_wunsch_gap_incentive
Help: Gap incentive value for inserting indels at cut sites
Type: int
Default: 1
Needleman Wunsch Alignment Matrix Location
--needleman_wunsch_aln_matrix_loc
Help: Location of the matrix specifying substitution scores in the NCBI format (see ftp://ftp.ncbi.nih.gov/blast/matrices/)
Type: str
Default: EDNAFULL
Plot Histogram Outliers
--plot_histogram_outliers
Help: If set, all values will be shown on histograms. By default (if unset), histogram ranges are limited to plotting data within the 99 percentile.
Type: bool
Default: False
Plot Window Size
--plot_window_size, --offset_around_cut_to_plot
Help: Defines the size of the window extending from the quantification window center to plot. Nucleotides within plot_window_size of the quantification_window_center for each guide are plotted.
Type: int
Default: 20
Min Frequency Alleles Around Cut To Plot
--min_frequency_alleles_around_cut_to_plot
Help: Minimum %% reads required to report an allele in the alleles table plot.
Type: float
Default: 0.2
Expand Allele Plots By Quantification
--expand_allele_plots_by_quantification
Help: If set, alleles with different modifications in the quantification window (but not necessarily in the plotting window (e.g. for another sgRNA)) are plotted on separate lines, even though they may have the same apparent sequence. To force the allele plot and the allele table to be the same, set this parameter. If unset, all alleles with the same sequence will be collapsed into one row.
Type: bool
Default: False
Allele Plot Percentages Only for Assigned Reference
--allele_plot_pcts_only_for_assigned_reference
Help: If set, in the allele plots, the percentages will show the percentage as a percent of reads aligned to the assigned reference. Default behavior is to show percentage as a percent of all reads.
Type: bool
Default: False
Quantification Window Coordinates
-qwc, --quantification_window_coordinates
Help: Bp positions in the amplicon sequence specifying the quantification window. This parameter overrides values of the '--quantification_window_center', '--cleavage_offset', '--window_around_sgrna' or '--window_around_sgrna' values. Any indels/substitutions outside this window are excluded. Indexes are 0-based, meaning that the first nucleotide is position 0. Ranges are separted by the dash sign (e.g. 'start-stop'), and multiple ranges can be separated by the underscore (_) (can be comma-separated list of values, corresponding to amplicon sequences given in --amplicon_seq e.g. 5-10,5-10_20-30 would specify the 6th-11th bp in the first reference and the 6th-11th and 21st-31st bp in the second reference). A value of 0 disables this filter for a particular amplicon (e.g. 0,90-110 This would disable the quantification window for the first amplicon and specify the quantification window of 90-110 for the second).Note that if there are multiple amplicons provided, and only one quantification window coordinate is provided, the same quantification window will be used for all amplicons and be adjusted to account for insertions/deletions.(default: None)
Type: str
Annotate Wildtype Allele
--annotate_wildtype_allele
Help: Wildtype alleles in the allele table plots will be marked with this string (e.g. **).
Type: str
Keep Intermediate
--keep_intermediate
Help: Keep all the intermediate files
Type: bool
Default: False
Dump
--dump
Help: Dump numpy arrays and pandas dataframes to file for debugging purposes
Type: bool
Default: False
Write Detailed Allele Table
--write_detailed_allele_table
Help: If set, a detailed allele table will be written including alignment scores for each read sequence.
Type: bool
Default: False
Fastq Output
--fastq_output
Help: If set, a fastq file with annotations for each read will be produced.
Type: bool
Default: False
Bam Output
--bam_output
Help: If set, a bam file with alignments for each read will be produced.
Type: bool
Default: False
Bowtie2 Index
-x, --bowtie2_index
Help: Basename of Bowtie2 index for the reference genome
Type: str
Zip Output
--zip_output
Help: If set, the output will be placed in a zip folder.
Type: bool
Default: False
Max Rows Alleles Around Cut To Plot
--max_rows_alleles_around_cut_to_plot
Help: Maximum number of rows to report in the alleles table plot.
Type: int
Default: 50
Suppress Report
--suppress_report
Help: Suppress output report
Type: bool
Default: False
Place Report In Output Folder
--place_report_in_output_folder
Help: If true, report will be written inside the CRISPResso output folder. By default, the report will be written one directory up from the report output.
Type: bool
Default: False
Suppress Plots
--suppress_plots
Help: Suppress output plots
Type: bool
Default: False
Base Editor Output
--base_editor_output
Help: Outputs plots and tables to aid in analysis of base editor studies.
Type: bool
Default: False
Conversion Nuc From
--conversion_nuc_from
Help: For base editor plots, this is the nucleotide targeted by the base editor
Type: str
Default: C
Conversion Nuc To
--conversion_nuc_to
Help: For base editor plots, this is the nucleotide produced by the base editor
Type: str
Default: T
Prime Editing Spacer Sequence
--prime_editing_pegRNA_spacer_seq
Help: pegRNA spacer sgRNA sequence used in prime editing. The spacer should not include the PAM sequence. The sequence should be given in the RNA 5'->3' order, so for Cas9, the PAM would be on the right side of the given sequence.
Type: str
Prime Editing Extension Sequence
--prime_editing_pegRNA_extension_seq
Help: Extension sequence used in prime editing. The sequence should be given in the RNA 5'->3' order, such that the sequence starts with the RT template including the edit, followed by the Primer-binding site (PBS).
Type: str
Prime Editing pegRNA Extension Quantification Window Size
--prime_editing_pegRNA_extension_quantification_window_size
Help: Quantification window size (in bp) at flap site for measuring modifications anchored at the right side of the extension sequence. Similar to the --quantification_window parameter, the total length of the quantification window will be 2x this parameter. Default: 5bp (10bp total window size)
Type: int
Default: 5
Prime Editing pegRNA Scaffold Sequence
--prime_editing_pegRNA_scaffold_seq
Help: If given, reads containing any of this scaffold sequence before extension sequence (provided by --prime_editing_extension_seq) will be classified as 'Scaffold-incorporated'. The sequence should be given in the 5'->3' order such that the RT template directly follows this sequence. A common value is 'GGCACCGAGUCGGUGC'.
Type: str
Prime Editing pegRNA Scaffold Min Match Length
--prime_editing_pegRNA_scaffold_min_match_length
Help: Minimum number of bases matching scaffold sequence for the read to be counted as 'Scaffold-incorporated'. If the scaffold sequence matches the reference sequence at the incorporation site, the minimum number of bases to match will be minimally increased (beyond this parameter) to disambiguate between prime-edited and scaffold-incorporated sequences.
Type: int
Default: 1
Prime Editing Nicking Guide Sequence
--prime_editing_nicking_guide_seq
Help: Nicking sgRNA sequence used in prime editing. The sgRNA should not include the PAM sequence. The sequence should be given in the RNA 5'->3' order, so for Cas9, the PAM would be on the right side of the sequence
Type: str
Prime Editing Override Prime Edited Reference Sequence
--prime_editing_override_prime_edited_ref_seq
Help: If given, this sequence will be used as the prime-edited reference sequence. This may be useful if the prime-edited reference sequence has large indels or the algorithm cannot otherwise infer the correct reference sequence.
Type: str
Prime Editing Override Sequence Checks
--prime_editing_override_sequence_checks
Help: If set, checks to assert that the prime editing guides and extension sequence are in the proper orientation are not performed. This may be useful if the checks are failing inappropriately, but the user is confident that the sequences are correct.
Type: bool
Default: False
CRISPResso 1 Mode
--crispresso1_mode
Help: Parameter usage as in CRISPResso 1
Type: bool
Default: False
dsODN
--dsODN
Help: Label reads with the dsODN sequence provided
Type: str
Auto
--auto
Help: Infer amplicon sequence from most common reads
Type: bool
Default: False
Debug
--debug
Help: Show debug messages
Type: bool
Default: False
No Rerun
--no_rerun
Help: Don't rerun CRISPResso2 if a run using the same parameters has already been finished.
Type: bool
Default: False
Number of Processes
-p, --n_processes
Help: Specify the number of processes to use for analysis. Please use with caution since increasing this parameter will significantly increase the memory required to run CRISPResso. Can be set to 'max'.
Type: str
Default: 1
Bam Input
--bam_input
Help: Aligned reads for processing in bam format
Type: str
BAM Chromosome Location
--bam_chr_loc
Help: Chromosome location in bam for reads to process. For example: 'chr1:50-100' or 'chrX'.
Type: str
Skip Failed
--skip_failed
Help: Continue with batch analysis even if one sample fails
Type: bool
Default: False
CRISPResso Command
--crispresso_command
Help: CRISPResso command to call
Type: str
Default: CRISPResso
Amplicons File
-f, --amplicons_file
Help: Amplicons description file. This file is a tab-delimited text file with up to 14 columns (2 required):
- amplicon_name: an identifier for the amplicon (must be unique).
- amplicon_seq: amplicon sequence used in the experiment.
- guide_seq (OPTIONAL): sgRNA sequence used for this amplicon without the PAM sequence. Multiple guides can be given separated by commas and not spaces.
- expected_hdr_amplicon_seq (OPTIONAL): expected amplicon sequence in case of HDR.
- coding_seq (OPTIONAL): Subsequence(s) of the amplicon corresponding to coding sequences. If more than one separate them by commas and not spaces.
- prime_editing_pegRNA_spacer_seq (OPTIONAL): pegRNA spacer sgRNA sequence used in prime editing. The spacer should not include the PAM sequence. The sequence should be given in the RNA 5'->3' order, so for Cas9, the PAM would be on the right side of the given sequence.
- prime_editing_nicking_guide_seq (OPTIONAL): Nicking sgRNA sequence used in prime editing. The sgRNA should not include the PAM sequence. The sequence should be given in the RNA 5'->3' order, so for Cas9, the PAM would be on the right side of the sequence.
- prime_editing_pegRNA_extension_seq (OPTIONAL): Extension sequence used in prime editing. The sequence should be given in the RNA 5'->3' order, such that the sequence starts with the RT template including the edit, followed by the Primer-binding site (PBS).
- prime_editing_pegRNA_scaffold_seq (OPTIONAL): If given, reads containing any of this scaffold sequence before extension sequence (provided by --prime_editing_extension_seq) will be classified as 'Scaffold-incorporated'. The sequence should be given in the 5'->3' order such that the RT template directly follows this sequence. A common value ends with 'GGCACCGAGUCGGUGC'.
- prime_editing_pegRNA_scaffold_min_match_length (OPTIONAL): Minimum number of bases matching scaffold sequence for the read to be counted as 'Scaffold-incorporated'. If the scaffold sequence matches the reference sequence at the incorporation site, the minimum number of bases to match will be minimally increased (beyond this parameter) to disambiguate between prime-edited and scaffold-incorporated sequences.
- prime_editing_override_prime_edited_ref_seq (OPTIONAL): If given, this sequence will be used as the prime-edited reference sequence. This may be useful if the prime-edited reference sequence has large indels or the algorithm cannot otherwise infer the correct reference sequence.
- quantification_window_coordinates (OPTIONAL): Bp positions in the amplicon sequence specifying the quantification window. This parameter overrides values of the '--quantification_window_center', '-- cleavage_offset', '--window_around_sgrna' or '-- window_around_sgrna' values. Any indels/substitutions outside this window are excluded. Indexes are 0-based, meaning that the first nucleotide is position 0. Ranges are separated by the dash sign like 'start-stop', and multiple ranges can be separated by the underscore (_). A value of 0 disables this filter. (can be comma-separated list of values, corresponding to amplicon sequences given in --amplicon_seq e.g. 5-10,5-10_20-30 would specify the 5th-10th bp in the first reference and the 5th-10th and 20th-30th bp in the second reference) (default: None)
- quantification_window_size (OPTIONAL): Defines the size (in bp) of the quantification window extending from the position specified by the '--cleavage_offset' or '--quantification_window_center' parameter in relation to the provided guide RNA sequence(s) (--sgRNA). Mutations within this number of bp from the quantification window center are used in classifying reads as modified or unmodified. A value of 0 disables this window and indels in the entire amplicon are considered. Default is 1, 1bp on each side of the cleavage position for a total length of 2bp.
- quantification_window_center (OPTIONAL): Center of quantification window to use within respect to the 3' end of the provided sgRNA sequence. Remember that the sgRNA sequence must be entered without the PAM. For cleaving nucleases, this is the predicted cleavage position. The default is -3 and is suitable for the Cas9 system. For alternate nucleases, other cleavage offsets may be appropriate, for example, if using Cpf1 this parameter would be set to 1. For base editors, this could be set to -17.
Type: str
Gene Annotations
--gene_annotations
Help: Gene Annotation Table from UCSC Genome Browser Tables (http://genome.ucsc.edu/cgi-bin/hgTables?command=start), please select as table 'knownGene', as output format 'all fields from selected table' and as file returned 'gzip compressed'
Type: str
Bowtie2 Options String
--bowtie2_options_string
Help: Override options for the Bowtie2 alignment command. By default, this is ' --end-to-end -N 0 --np 0 -mp 3,2 --score-min L,-5,-3(1-H)' where H is the default homology score.
Type: str
Use Legacy Bowtie2 Options String
--use_legacy_bowtie2_options_string
Help: Use legacy (more stringent) Bowtie2 alignment parameters: ' -k 1 --end-to-end -N 0 --np 0 '.
Type: bool
Default: False
Minimum Reads to Use Region
--min_reads_to_use_region
Help: Minimum number of reads that align to a region to perform the CRISPResso analysis
Type: float
Default: 1000
Skip Reporting Problematic Regions
--skip_reporting_problematic_regions
Help: Skip reporting of problematic regions. By default, when both amplicons (-f) and genome (-x) are provided, problematic reads that align to the genome but to positions other than where the amplicons align are reported as problematic
Type: bool
Default: False
Compile Postrun References
--compile_postrun_references
Help: If set, a file will be produced which compiles the reference sequences of frequent amplicons.
Type: bool
Default: False
Compile Postrun Reference Allele Cutoff
--compile_postrun_reference_allele_cutoff
Help: Only alleles with at least this percentage frequency in the population will be reported in the postrun analysis. This parameter is given as a percent, so 30 is 30%%.
Type: float
Default: 30
Alternate Alleles
--alternate_alleles
Help: Path to tab-separated file with alternate allele sequences for pooled experiments. This file has the columns 'region_name','reference_seqs', and 'reference_names' and gives the reference sequences of alternate alleles that will be passed to CRISPResso for each individual region for allelic analysis. Multiple reference alleles and reference names for a given region name are separated by commas (no spaces).
Type: str
Limit Open Files For Demux
--limit_open_files_for_demux
Help: If set, only one file will be opened during demultiplexing of read alignment locations. This will be slightly slower as the reads must be sorted, but may be necessary if the number of amplicons is greater than the number of files that can be opened due to OS constraints.
Type: bool
Default: False
Aligned Pooled Bam
--aligned_pooled_bam
Help: 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 if the aligned reads are paired-end sequenced, they should already be merged into 1 read (e.g. via Flash) before alignment.
Type: str
Demultiplex Only At Amplicons
--demultiplex_only_at_amplicons
Help: DEPRECATED in v2.3.2, see demultiplex_at_amplicons_and_genome
Type: bool
Default: False
Demultiplex Genome Wide
--demultiplex_genome_wide
Help: If set, and an amplicon file (--amplicons_file) and reference sequence (--bowtie2_index) are provided, the entire genome will be demultiplexed and reads with the exact same start and stop coordinates as an amplicon will be assigned to that amplicon. If this flag is not set, reads overlapping alignment positions of amplicons will be demultiplexed and assigned to that amplicon.
Type: bool
Default: False
Disable Guardrails
--disable_guardrails
Help: Disable guardrail warnings
Type: bool
Default: False
Use Matplotlib
--use_matplotlib
Help: Use matplotlib for plotting instead of plotly/d3 when CRISPRessoPro is installed
Type: bool
Default: False