UDiTaS™, a genome editing detection method for indels and genome rearrangements

DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

(2017) Lixin Chen et al.   SCIENCE

Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus

(2017) Anne Bothmer et al.   Nature Communications

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

(2016) Josh Tycko et al.   MOLECULAR CELL

Detecting DNA double-stranded breaks in mammalian genomes by linear amplification–mediated high-throughput genome-wide translocation sequencing

(2016) Jiazhi Hu et al.   Nature Protocols

Basal exon skipping and genetic pleiotropy: A predictive model of disease pathogenesis

(2015) Theodore G. Drivas et al.   Science Translational Medicine

Quantifying on- and off-target genome editing

(2015) Ayal Hendel et al.   TRENDS IN BIOTECHNOLOGY

Comparison of T7E1 and Surveyor Mismatch Cleavage Assays to Detect Mutations Triggered by Engineered Nucleases

(2015) Léna Vouillot et al.   G3-Genes Genomes Genetics

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Chromosomal Translocations in Human Cells Are Generated by Canonical Nonhomologous End-Joining

(2014) Hind Ghezraoui et al.   MOLECULAR CELL

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

Anchored multiplex PCR for targeted next-generation sequencing

(2014) Zongli Zheng et al.   NATURE MEDICINE

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Tagmentation-based whole-genome bisulfite sequencing

(2013) Qi Wang et al.   Nature Protocols

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

(2011) Roberto Chiarle et al.   CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS