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Bioinformatics. 2017 Sep 15;33(18):2963-2965. doi: 10.1093/bioinformatics/btx335.

CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution.

Jeong HH1,2, Kim SY1,2, Rousseaux MWC1,2, Zoghbi HY1,2,3,4, Liu Z2,3.

Author information

1
Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA.
2
Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
3
Department of Pediatrics.
4
Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA.

Abstract

Summary:

We present a user-friendly, cloud-based, data analysis pipeline for the deconvolution of pooled screening data. This tool, CRISPRcloud, serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing files derived from pooled screening experiments while at the same time presenting them in a user-friendly way on a secure web-based platform. Moreover, CRISPRcloud serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets. Taken together, the framework described in this study is expected to accelerate development of web-based bioinformatics tool for handling all studies which include next generation sequencing data.

Availability and implementation:

http://crispr.nrihub.org.

Contact:

zhandong.liu@bcm.edu.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28541456
PMCID:
PMC5870715
DOI:
10.1093/bioinformatics/btx335
[Indexed for MEDLINE]
Free PMC Article

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