Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries

• Published in: STAR protocols 2023-03, Vol.4 (1), p.102027, Article 102027
• Main Authors: Pascarella, Giovanni, Straniero, Letizia, Frith, Martin, Carninci, Piero
• Format: Article
• Language: English
• Subjects: Bioinformatics; Genomics; Molecular Biology; Protocol; Sequencing
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2022.102027

Recombination of repeat elements is an important source of genomic variation in human tissues. Here, we describe steps to prepare libraries enriched for repeat elements starting from the genomic DNA of any species. We also detail the computational post-processing of the TE-reX pipeline output to generate datasets of putative somatic and polymorphic recombination events. For complete details on the use and execution of this protocol, please refer to Pascarella et al. (2022). [Display omitted] •Perform Capture-seq for robust enrichment of repeat sequences from any genomic DNA•From genomic DNA to sequencing-ready libraries in approximately one day•Identify recombination of repeat elements from short- and long-DNA reads•Generate BED-like datasets for downstream analyses from TE-reX output Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Recombination of repeat elements is an important source of genomic variation in human tissues. Here, we describe steps to prepare libraries enriched for repeat elements starting from the genomic DNA of any species. We also detail the computational post-processing of the TE-reX pipeline output to generate datasets of putative somatic and polymorphic recombination events.