FiberHMM 3.0.0

FiberHMM 3.0 is the third generation of the FiberHMM family, released together
with FiberBrowser 3.0.0 (which requires fiberhmm>=3.0,<4).

The emission tables have been updated, so re-run calls made with earlier
versions. fiberhmm-check <outputs> lists which of your BAMs, QC reports,
posteriors files and consensus results need re-running.

Highlights

• 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.

Full changes: CHANGELOG · Docs: https://fiberseq.github.io/FiberHMM/

pip install fiberhmm==3.0.0