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Sci Rep 2016 Jan 22;6:30330. doi: 10.1038/srep30330.
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BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment.

Boel A , Steyaert W , De Rocker N , Menten B , Callewaert B , De Paepe A , Coucke P , Willaert A .

Targeted mutagenesis by the CRISPR/Cas9 system is currently revolutionizing genetics. The ease of this technique has enabled genome engineering in-vitro and in a range of model organisms and has pushed experimental dimensions to unprecedented proportions. Due to its tremendous progress in terms of speed, read length, throughput and cost, Next-Generation Sequencing (NGS) has been increasingly used for the analysis of CRISPR/Cas9 genome editing experiments. However, the current tools for genome editing assessment lack flexibility and fall short in the analysis of large amounts of NGS data. Therefore, we designed BATCH-GE, an easy-to-use bioinformatics tool for batch analysis of NGS-generated genome editing data, available from BATCH-GE detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies for a large number of samples in parallel. Furthermore, this new tool provides flexibility by allowing the user to adapt a number of input variables. The performance of BATCH-GE was evaluated in two genome editing experiments, aiming to generate knock-out and knock-in zebrafish mutants. This tool will not only contribute to the evaluation of CRISPR/Cas9-based experiments, but will be of use in any genome editing experiment and has the ability to analyze data from every organism with a sequenced genome.

PubMed ID: 27461955
PMC ID: PMC4962088
Article link: Sci Rep

Species referenced: Xenopus
Genes referenced: kit pls3 slc2a10 tprkb

Article Images: [+] show captions
References [+] :
Auer, CRISPR/Cas9 and TALEN-mediated knock-in approaches in zebrafish. 2014, Pubmed