PUBLICATION
BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment
- Authors
- Boel, A., Steyaert, W., De Rocker, N., Menten, B., Callewaert, B., De Paepe, A., Coucke, P., Willaert, A.
- ID
- ZDB-PUB-160728-5
- 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.
Citation
Boel, A., Steyaert, W., De Rocker, N., Menten, B., Callewaert, B., De Paepe, A., Coucke, P., Willaert, A. (2016) BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment. Scientific Reports. 6:30330.
Abstract
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.
Errata / Notes
This article is corrected by ZDB-PUB-220906-121 .
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping