Tn5-based chromatin footprinting and regulatory motif analysis

fp-tools analyzes bulk and single-cell ATAC-seq (assay for transposase-accessible chromatin using sequencing) data. It corrects sequence bias, scores footprints around DNA motifs, and compares samples or cell groups. Use the command-line interface (CLI) or graphical user interface (GUI).

A footprint or motif match does not prove transcription factor (TF) binding. CUT&Tag (cleavage under targets and tagmentation) needs assay-specific controls and interpretation.

New to these file formats? See the practical glossary.

PyPI GitHub Python 3.11–3.13 MIT license

Choose your starting point:

• BAM/BAI and peak BED files: follow the runnable bulk ATAC-seq workflow.
• Single-cell fragments: follow the single-cell workflow.
• Existing fp-tools outputs: open the output demo or choose a command in the tool overview.

Linux command-line and container users can optionally prepare FASTQ files with prepare-atac.

Install fp-tools  ·  View the tool overview