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FiberHMM

FiberHMM calls chromatin footprints on single DNA molecules. From the modification marks of a Fiber-seq (m6A) or DAF-seq (deamination) read it finds the protected stretches (nucleosomes, and transcription-factor or Pol II footprints) and the accessible stretches between them (methylase-sensitive patches, MSPs). Its calls are written back into the BAM as standard tags that fibertools, FIRE and FiberBrowser, the companion browser (install with pip install fiberbrowser), read.

Across many molecules, FiberHMM also finds recurrent footprint classes at a locus and measures how often each molecule carries each one.

FiberHMM 3.0

3.0 is the third generation of the FiberHMM family and is released together with FiberBrowser 3.0. 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.

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.

What it does

Stage Command Page
Call nucleosomes, MSPs and TF footprints on every read fiberhmm-call Calling footprints
Re-call TFs or nucleosomes on an already called BAM fiberhmm-recall-tfs, fiberhmm-recall-nucs Re-calling
DAF-seq extras: duplicates, SNPs, R/Y encoding, CpG-island methylation fiberhmm-dedup, -daf-snps, -daf-encode, -tag-m5c, -call-m5c DAF-seq
Pair the two strands of one scDAF molecule and call them jointly fiberhmm-pair Duplex
Check a run against reference data sets fiberhmm-qc (also automatic after fiberhmm-call) Quality control
Export calls as BED12 / bigBed tracks fiberhmm-extract Extracting tracks
Find footprint classes across molecules and measure them per molecule fiberhmm-consensus Footprint classes
Measure frozen classes in new data or at other loci fiberhmm-transfer Transferring classes
Rescue footprints missed on one strand, using the other strand fiberhmm-strand-rescue Strand rescue
Footprint population model from per-read TF calls fiberhmm-footprint-model Footprint population model
Per-position HMM posteriors fiberhmm-posteriors Posteriors
Build a model for a new chemistry or condition fiberhmm-probs, fiberhmm-train, fiberhmm-utils Training a model

Supported data

Chemistry Platform fiberhmm-call preset
Hia5 Fiber-seq (m6A) PacBio --enzyme hia5 --seq pacbio
Hia5 Fiber-seq (m6A) Oxford Nanopore --enzyme hia5 --seq nanopore
DddB DAF-seq (deamination) any (usually Nanopore) --enzyme dddb
DddA DAF-seq (deamination) any (usually PacBio) --enzyme ddda

Models for these four are bundled. Other chemistries (EcoGII, GpC/CpG methyltransferases) are development-only; see Chemistries and platforms.

Where to start