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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

 (25)
library_books

Functional significance of co occurring mutations in PIK3CA and MAP3K1 in breast cancer

2018
PMCID: 5940413
PMID: 29765551
DOI: 10.18632/oncotarget.25118

[…] paired-end sequencing using a nextseq500 ngs instrument (illumina). finally, sequencing reads were automatically de-multiplexed using nextseq500 instrument and paired fastq files were analyzed using crispresso []. the frequency of mutated alleles among ngs reads were calculated based on the crispresso's detected alleles ()., cells were transiently transfected using lipofectamine rnaimax […]

library_books

Somatic genome editing with the RCAS TVA CRISPR Cas9 system for precision tumor modeling

2018
PMCID: 5899147
PMID: 29654229
DOI: 10.1038/s41467-018-03731-w

[…] by spin-column clean-up and sequenced, using the braf_seq oligo (supplementary table ), on an illumina platform by following manufacturer’s protocols. fastq reads files were analyzed with the crispresso web application (http://www.crispresso.rocks)., nestin-tv-a and gfap-tv-a, were generously provided by eric holland. rosa26-lsl-cas9 knockin mouse strain was purchased from the jackson […]

library_books

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

2018
PMCID: 5870970
PMID: 29584750
DOI: 10.1371/journal.pone.0193818

[…] 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., for chip assays transfected cells were cross-linked 48 hours post transfection by incubation with 1% formaldehyde solution […]

library_books

Therapeutic Genome Editing With CRISPR/Cas9 in a Humanized Mouse Model Ameliorates α1 antitrypsin Deficiency Phenotype

2018
PMCID: 5925576
PMID: 29500128
DOI: 10.1016/j.ebiom.2018.02.015

[…] run using paired-end chemistry with 150 bp read length., sequencing reads were automatically de-multiplexed using nextseq500 instrument (illumina) and paired fastq files were analyzed using crispresso (). briefly, reads with a minimum average quality score of 33 were aligned to the reference sequence. a window of 50 base pair centered on the predicted cleavage site was specified […]

library_books

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

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

[…] was sequenced on a illumina miseq (illumina, san diego, ca) with v2 chemistry using a 500 cycles kit according to the manufacturer’s instructions. deep sequencing data was analyzed using the tool crispresso []., statistical analysis was performed using graph pad prism® (version 7.00; graphpad software, inc, la jolla, ca). significance was calculated using unpaired one-way anova with multiple […]

library_books

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

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

[…] and gray matter. these latter cell populations, which are much more numerous than motor neurons, were not expected to be gene-modified on the basis of our immunohistochemistry results. according to crispresso (a software pipeline that analyzes genome editing outcomes from deep sequencing data) (), indels were present in ~0.2 and ~0.4% of sequenced hsod1g93a transgenes from the lumbar […]


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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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