FiberHMM

Chromatin footprint calling on single DNA molecules from Fiber-seq (m6A) and DAF-seq (deamination) data. For every read, FiberHMM calls nucleosomes, transcription-factor and other sub-nucleosomal footprints, and the methylase-sensitive patches (MSPs) between them, using sequence-context-aware emission models; across molecules, it finds recurrent footprint classes and measures how often each molecule carries them. Calls are written into the BAM as fibertools-compatible ns/nl/as/al and Molecular-annotation MA/AQ tags, readable by ft, FIRE and FiberBrowser.

Documentation: fiberseq.github.io/FiberHMM (source in docs/).

FiberHMM 3.0 is the third generation of the FiberHMM family, released with FiberBrowser 3.0.0. The emission tables have been updated, so re-run calls made with earlier versions. fiberhmm-check <your outputs> lists which files need re-running. See Upgrading from 2.x and the CHANGELOG.

What's new in 3.0

DddA nucleosomes follow the helical phase. DddA (SsDddA, scDAF-seq) also deaminates inside nucleosomes, in step with the ~10-bp helical phase of the wrapped DNA. fiberhmm-call --enzyme ddda now places nucleosomes with a phase-aware rotational model, so internal deaminations no longer break nucleosomes into pieces.
scDAF duplexes. fiberhmm-pair finds the two strands (CT and GA reads) of one DddA molecule and calls footprints on both strands jointly. The DddA TF emission table is recalibrated in chromatin on physical scDAF duplexes.
CpG-island methylation from deamination. fiberhmm-tag-m5c calls each molecule's CpG islands as methylated or unmethylated, and fiberhmm-call-m5c calls methylated and unmethylated domains across molecules. For DddA, CpGs are masked by default outside confidently unmethylated islands, in the first-pass HMM and in footprint recall (--use-m5c, --cpg-mask-policy).
Cleaner DAF input. Adjacent CC/GG targets are thinned to one (keep-one, on for DddA), strand-swap chimeras are filtered, and PCR duplicates are marked by deamination pattern.
fiberhmm-pipeline goes from reads and a reference (FASTA or plasmid map) to a called BAM ready for FiberBrowser in one command.
fiberhmm-check reads your existing outputs and lists which ones need re-running, with the command to use.
Updated emission tables. The Nanopore Hia5 table is rebuilt from matched controls and DddB has a new in-vivo table.
Footprint classes. fiberhmm-consensus finds recurrent footprint classes across molecules and measures them per molecule, and fiberhmm-transfer measures frozen classes in new data.
Python 3.10 to 3.14.

Install

pip install fiberhmm              # Python 3.10 to 3.14
pip install "fiberhmm[all]"       # plus QC figures (matplotlib) and HDF5 posteriors (h5py)

Quick start

# DAF-seq amplicons / plasmids: reads + reference in, FiberBrowser-ready calls out
fiberhmm-pipeline reads.fastq.gz --reference plasmid.dna --enzyme dddb -o run/

# Aligned BAMs
fiberhmm-call -i aligned.bam -o calls.bam --enzyme hia5 --seq pacbio -c 8 --region-parallel   # Hia5 PacBio
fiberhmm-call -i aligned.bam -o calls.bam --enzyme hia5 --seq nanopore -c 8 --region-parallel # Hia5 Nanopore
fiberhmm-call -i aligned.bam -o calls.bam --enzyme dddb -c 8 --region-parallel                # DddB DAF-seq (DddA: --enzyme ddda)
fiberhmm-extract -i calls.bam -o tracks/                                                     # BED12 / bigBed tracks

A synthetic demo data set and a walk-through of every chemistry are in the Quick start.

Documentation

Getting started: installation, quick start, choosing --enzyme and --seq
Concepts: how FiberHMM works, chemistries and platforms, coordinate frames, tags and scores
Workflows: calling, re-calling, DAF-seq, plasmids, duplex pairing, tracks, posteriors, QC, footprint classes (fiberhmm-consensus), transfer, strand rescue, training
Reference: every command and option, BAM tags, header declarations, footprint-tag frames, checking outputs for re-runs (fiberhmm-check), bundled models, consensus output files, Python API, environment variables
Troubleshooting

License

MIT; see LICENSE. Citing FiberHMM.

Metadata

Release files for fiberhmm 3.0.1

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Source distribution (sdist)

Source distribution for fiberhmm 3.0.1
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Table of built distributions (wheels) for fiberhmm 3.0.1
File	Interpreter	ABI	Platform	Reset
fiberhmm-3.0.1-py3-none-any.whl 3.2 MB Oct 16, 2026	Python 3	none	any	Details

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