ZFIN ID: ZDB-PUB-160728-5
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.
Date: 2016
Source: Scientific Reports   6: 30330 (Journal)
Registered Authors: Coucke, Paul, Willaert, Andy
Keywords: Genetic engineering, High-throughput screening
MeSH Terms:
  • Animals
  • CRISPR-Cas Systems
  • Gene Editing/methods*
  • High-Throughput Nucleotide Sequencing/methods*
  • INDEL Mutation
  • Sequence Analysis, DNA/methods*
  • Software*
  • Zebrafish
  • Zebrafish Proteins/genetics
PubMed: 27461955 Full text @ Sci. Rep.
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 https://github.com/WouterSteyaert/BATCH-GE.git. 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.