A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data

Allele-specific alignment sorting

Transposon Insertion Finder - Detection of new TE insertions in NGS data

computational tool to identify trasposable element insertions using Hi-C data

Transposable Element Finder - Detection of active transposable elements from NGS data

ATAC-seq Profiler with Spike-in