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ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs.

ABSTRACT:

Summary

CRISPR screens are increasingly performed to associate genotypes with genotypes. So far, however, their analysis required specialized computational knowledge to transform high-throughput next-generation sequencing (NGS) data into sequence formats amenable for downstream analysis. We developed ReCo, a stand-alone and user-friendly analytics tool for generating read-count tables of single and combinatorial CRISPR library and screen-based NGS data. Together with cutadapt and bowtie2 for rapid sequence trimming and alignment, ReCo enables the automated generation of read count tables from staggered NGS reads for the downstream identification of gRNA-induced phenotypes.

Availability and implementation

ReCo is published under the MIT license and available at: https://github.com/KaulichLab/ReCo.

SUBMITTER: Wegner M

PROVIDER: S-EPMC10400375 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs.

Wegner Martin M Kaulich Manuel M

Bioinformatics (Oxford, England) 20230801 8

<h4>Summary</h4>CRISPR screens are increasingly performed to associate genotypes with genotypes. So far, however, their analysis required specialized computational knowledge to transform high-throughput next-generation sequencing (NGS) data into sequence formats amenable for downstream analysis. We developed ReCo, a stand-alone and user-friendly analytics tool for generating read-count tables of single and combinatorial CRISPR library and screen-based NGS data. Together with cutadapt and bowtie2 ...[more]

PMID: 37481709

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