ChIP-seq analysis Tools

F-Seq2 is a Python-based peak caller for high-throughput sequencing data (ChIP-seq, DNase-seq, ATAC-seq) that uses kernel density estimation combined with a local Poisson statistical framework to identify biologically meaningful genomic regions.

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.

epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use. It also contains a reimplementation of the SICER-df scripts for differential enrichment and a script to create many kinds of bigwigs from your data.