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Protocols

CRISPResso specifications

Information


Unique identifier OMICS_10601
Name CRISPResso
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Paired-end reads (two files) or single-end reads (single file) from a deep sequencing experiment and a reference amplicon sequence.
Input format FASTQ
Output data A set of informative graphs that allow for the quantification and visualization of the position and type of outcomes within an amplicon sequence.
Operating system Unix/Linux
Programming languages Python
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
Requirements
Java, C compiler / make
Maintained Yes

Subtools


  • CRISPRessoCompare
  • CRISPRessoPooled
  • CRISPRessoPooledCompare
  • CRISPRessoWGS

Download


download.png
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Versioning


No version available

Documentation


Maintainers


  • person_outline Guo-Cheng Yuan
  • person_outline Luca Pinello
  • person_outline Daniel Bauer

Information


Unique identifier OMICS_10601
Name CRISPResso
Interface Web user interface
Restrictions to use None
Input data Paired-end reads (two files) or single-end reads (single file) from a deep sequencing experiment and a reference amplicon sequence.
Input format FASTQ
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • CRISPRessoCompare
  • CRISPRessoPooled
  • CRISPRessoPooledCompare
  • CRISPRessoWGS

Download


github.png

Documentation


Maintainers


  • person_outline Guo-Cheng Yuan
  • person_outline Luca Pinello
  • person_outline Daniel Bauer

Publication for CRISPResso

CRISPResso citations

 (17)
call_split

Unexpected binding behaviors of bacterial Argonautes in human cells cast doubts on their use as targetable gene regulators

2018
PLoS One
PMCID: 5870970
PMID: 29584750
DOI: 10.1371/journal.pone.0193818
call_split See protocol

[…] ASTX barcode splitter by identifying barcodes at the beginning or the reverse complement barcodes at the end of sequence reads, allowing for one mismatch. Processed fastq files were analyzed with the CRISPResso online tool (http://crispresso.rocks) using default settings. […]

library_books

Acute multi sgRNA knockdown of KEOPS complex genes reproduces the microcephaly phenotype of the stable knockout zebrafish model

2018
PLoS One
PMCID: 5773193
PMID: 29346415
DOI: 10.1371/journal.pone.0191503

[…] ion of individual animal and amplicon. Deep sequencing data were generated using the Illumina MiSeq platform. Sequencing data were analyzed for all specific mutations induced by sgRNAs using the tool CRISPResso []. CRISPResso analysis was performed individually per animal and the output was combined for the further calculations. The input parameters included the amplicon reference sequence (derive […]

library_books

In vivo genome editing improves motor function and extends survival in a mouse model of ALS

2017
Sci Adv
PMCID: 5738228
PMID: 29279867
DOI: 10.1126/sciadv.aar3952

[…] oates Genomics Sequencing Laboratory). Multiplexed samples were deconvoluted on the basis of unique barcodes, and adapter sequences were trimmed from the reads. Indel quantitation was performed using CRISPResso (). Sequences were filtered for >99% confidence (phred33 ≥ 20) per read. Sequence alignment was performed on filtered reads using EMBOSS Needle using the default CRISPResso settings. Indels […]

call_split

Structural basis for genome wide recognition of 5 bp GC motifs by SMAD transcription factors

2017
Nat Commun
PMCID: 5727232
PMID: 29234012
DOI: 10.1038/s41467-017-02054-6
call_split See protocol

[…] reased viability through FACS 72 h post transfection. Mutant clones were first screened through aberrant melting temperature of qPCR products, then verified by PCR, TA cloning, Sanger sequencing, and CRISPResso analysis individually. The mESCs used for this experiment are diploid. […]

library_books

Methods for Scarless, Selection Free Generation of Human Cells and Allele Specific Functional Analysis of Disease Associated SNPs and Variants of Uncertain Significance

2017
Sci Rep
PMCID: 5678142
PMID: 29118424
DOI: 10.1038/s41598-017-15407-4

[…] , single long reads were demultiplexed by identifying barcodes at the beginning or end of the sequence read, allowing for one mismatch. Processed fastq files were analyzed for NHEJ frequency with the CRISPResso online tool (http://crispresso.rocks) using default settings. For increased stringency, HDR-positive reads were identified from fastq files using the grep function to select reads with 100% […]

library_books

Targeted mutagenesis in a human parasitic nematode

2017
PLoS Pathog
PMCID: 5650185
PMID: 29016680
DOI: 10.1371/journal.ppat.1006675

[…] ts in large deletions rather than small indels at the target locus. To further confirm the lack of small indels, we analyzed indel frequency in the deep-sequencing samples using the CRISPRessoWGS and CRISPRessoCompare computational suite []. The CRISPRessoWGS program is designed to analyze deep-sequencing reads aligned to a reference genome and quantify CRISPR-Cas9-editing outcomes, such as indels […]

Citations

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CRISPResso institution(s)
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA; Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Department of Microbiology, Immunology, and Molecular Genetics, Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Howard Hughes Medical Institute, Boston, MA, USA
CRISPResso funding source(s)
Supported by NHGRI Career Development Award K99HG008399, F30DK103359-01A1, P01HL032262, P30DK049216 (Center of Excellence in Molecular Hematology), NIDDK Career Development Award K08DK093705, Doris Duke Charitable Foundation, Charles H. Hood Foundation, Cooley’s Anemia Foundation, American Society of Hematology, Burroughs Wellcome Fund, NIH R01HL119099 and R01HG005085.

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