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

Hyun-Hwan Jeong; Seon Young Kim; Maxime W C Rousseaux; Huda Y Zoghbi; Zhandong Liu

doi:10.1093/bioinformatics/btx335

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

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

Authors

Hyun-Hwan Jeong^{1

2}, Seon Young Kim^{1

2}, Maxime W C Rousseaux^{1

2}, Huda Y Zoghbi^{1

2

3

4}, Zhandong Liu^{2

3}

Affiliations

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.

MeSH terms

Clustered Regularly Interspaced Short Palindromic Repeats
Computational Biology / methods*
High-Throughput Nucleotide Sequencing / methods*
Sequence Analysis, DNA
Software*

Grants and funding

R01 GM120033/GM/NIGMS NIH HHS/United States