Identification of genome edited cells using CRISPRnano.
Thach NguyenHaribaskar RamachandranSoraia MartinsJean KrutmannAndrea RossiPublished in: Nucleic acids research (2022)
Genome engineering-induced cleavage sites can be resolved by non-homologous end joining (NHEJ) or homology-directed repair (HDR). Identifying genetically modified clones at the target locus remains an intensive and laborious task. Different workflows and software that rely on deep sequencing data have been developed to detect and quantify targeted mutagenesis. Nevertheless, these pipelines require high-quality reads generated by Next Generation Sequencing (NGS) platforms. Here, we have developed a robust, versatile, and easy-to-use computational webserver named CRISPRnano (www.CRISPRnano.de) that enables the analysis of low-quality reads generated by affordable and portable sequencers including Oxford Nanopore Technologies (ONT) devices. CRISPRnano allows fast and accurate identification, quantification, and visualization of genetically modified cell lines, it is compatible with NGS and ONT sequencing reads, and it can be used without an internet connection.
Keyphrases
- crispr cas
- dna repair
- induced apoptosis
- single cell
- bioinformatics analysis
- genome wide
- cell cycle arrest
- high glucose
- diabetic rats
- electronic health record
- high resolution
- copy number
- healthcare
- health information
- big data
- endoplasmic reticulum stress
- quality improvement
- cell death
- machine learning
- drug delivery
- mass spectrometry
- cell proliferation
- transcription factor
- deep learning
- stress induced
- cell free