Fig. 2

RepEnTools has scripts for automated installation, data analysis and plotting figures for rapid RE enrichment analysis of ChIP-seq on the human chm13v2 genome assembly. A RepEnTools in UNIX contains scripts to easily install all components, retrieve all necessary data for analysis using the human chm13v2 genome assembly and also the option to run in demonstration mode. The demo mode RepEnTools dataset is a reduced-size (200K reads per file) version of the UHRF1-TTD CIDOP dataset (GSE213741) providing two biological replicates. B Simplified workflow of the automated repeat enrichment analysis by the RepEnTools ~ $ ret script in UNIX. The FASTQ files (yellow) of two biological replicates of ChIP-seq and corresponding Input chromatin must be provided by the user with standardised names, and RepEnTools provides the repeat masker (rmsk) file for chm13v2 (blue). The white boxes indicate the data processing steps. Our Python scripts for data analysis are in light orange, and the tabular outputs are in green. Each programme is run in an individual miniconda environment, managing the changing dependencies. The ~ $ ret script regulates the conda environments, the bioinformatics packages that RepEnTools uses, the Python scripts written specifically for RepEnTools, and all subsequent steps. See also Additional file 1: Fig. S2C. C RepEnTools in UNIX is rapidly installed, and ready for use on a new UNIX system. Analysis of a full-size dataset (comprising 2 CIDOP + 2 Input FASTQ files) was consistently completed in under 105 min, using commodity hardware. Testing was conducted on a 64-bit, Intel i5-6500 @ 3.2 GHz × 4 (2015), 16 GB RAM, 1TB HDD desktop running freshly installed Ubuntu 23.04 or Debian 12.2