RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats

Table 1 Overview of key features of the principal previous programmes for repeat enrichment analysis of ChIP-seq data and RepEnTools

	Repeat Enrichment Estimator [16]	RepEnrich [17]	Teissandier et al. [18]	RepEnTools (This study)
Year	2010	2014	2019	2023
Genome	hg18 & RE pseudo-genome	hg19 & RE pseudo-genome	Not reported	chm13v2.0 (T2T)
Aligner	Modified SeqMap & bwa	Bowtie1	STAR	HISAT2
RMSK annotation	Standard & Repbase canonical & instances	Standard & instances	Standard & LTR dictionary	Adjusted standard
Normalisation to library size	✓	✓	-	✓
Use of input	Optional	Manual option	-	✓
Replicate analysis	-	manual option	-	✓
Environment	UNIX	UNIX	UNIX	Galaxy/UNIX
Installation requirements	Source code & dependencies	Source code & individual programmes & dependencies (conda)	Individual programmes & dependencies	None on public Galaxy servers, Auto-installer for individual programmes & dependencies (UNIX)
raw FASTQ → plots	-	-	-	✓

Repeat element (RE) enrichment analysis within short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task. In the past, certain publications paved the way for RE enrichment analysis [16,17,18]. RepEnTools substantially improves upon those programmes, using the landmark chm13v2.0 (T2T) human assembly, the corresponding RMSK annotation, and an improved aligner. Normalisations, usage of input for enrichment analysis and usage of two experimental replicates for statistics on enrichment reproducibility reduce biases and put the data in meaningful context. RepEnTools comes as a complete analysis package that can be auto-installed in a UNIX environment or used on Galaxy servers. In either case, the only required input is to define the files to be used and the maximum fragment size for each FASTQ. The scripts incorporated in the UNIX implementation will then output all the necessary files, including tables and plots of enrichment. The Galaxy workflows we provide are supplemented by a spreadsheet to easily perform the table operations and generate the plots

ISSN: 1759-8753